Name: rs1555398616
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs1555398616

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:58507255-58507257 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delGT / dupGT
Variation Type: Indel Insertion and Deletion
Frequency: delGT=0.00000 (0/11862, ALFA)
dupGT=0.00000 (0/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KIAA0586 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HWEP
Total	Global	11862	TGT=1.00000	T=0.00000, TGTGT=0.00000	1.0	N/A
European	Sub	7618	TGT=1.0000	T=0.0000, TGTGT=0.0000	1.0	N/A
African	Sub	2816	TGT=1.0000	T=0.0000, TGTGT=0.0000	1.0	N/A
African Others	Sub	108	TGT=1.000	T=0.000, TGTGT=0.000	1.0	N/A
African American	Sub	2708	TGT=1.0000	T=0.0000, TGTGT=0.0000	1.0	N/A
Asian	Sub	108	TGT=1.000	T=0.000, TGTGT=0.000	1.0	N/A
East Asian	Sub	84	TGT=1.00	T=0.00, TGTGT=0.00	1.0	N/A
Other Asian	Sub	24	TGT=1.00	T=0.00, TGTGT=0.00	1.0	N/A
Latin American 1	Sub	146	TGT=1.000	T=0.000, TGTGT=0.000	1.0	N/A
Latin American 2	Sub	610	TGT=1.000	T=0.000, TGTGT=0.000	1.0	N/A
South Asian	Sub	94	TGT=1.00	T=0.00, TGTGT=0.00	1.0	N/A
Other	Sub	470	TGT=1.000	T=0.000, TGTGT=0.000	1.0	N/A

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
Allele Frequency Aggregator	Total	Global	11862	TGT=1.00000	delGT=0.00000, dupGT=0.00000
Allele Frequency Aggregator	European	Sub	7618	TGT=1.0000	delGT=0.0000, dupGT=0.0000
Allele Frequency Aggregator	African	Sub	2816	TGT=1.0000	delGT=0.0000, dupGT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	TGT=1.000	delGT=0.000, dupGT=0.000
Allele Frequency Aggregator	Other	Sub	470	TGT=1.000	delGT=0.000, dupGT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	TGT=1.000	delGT=0.000, dupGT=0.000
Allele Frequency Aggregator	Asian	Sub	108	TGT=1.000	delGT=0.000, dupGT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	TGT=1.00	delGT=0.00, dupGT=0.00

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 14	NC_000014.9:g.58507256_58507257del
GRCh38.p14 chr 14	NC_000014.9:g.58507256_58507257dup
GRCh37.p13 chr 14	NC_000014.8:g.58973974_58973975del
GRCh37.p13 chr 14	NC_000014.8:g.58973974_58973975dup
KIAA0586 RefSeqGene (LRG_1096)	NG_051335.2:g.84872_84873del
KIAA0586 RefSeqGene (LRG_1096)	NG_051335.2:g.84872_84873dup

Gene: KIAA0586, KIAA0586 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KIAA0586 transcript variant 1	NM_001244189.2:c.4328-129… NM_001244189.2:c.4328-1299_4328-1298del	N/A	Intron Variant
KIAA0586 transcript variant 2	NM_001244190.2:c.4124-129… NM_001244190.2:c.4124-1299_4124-1298del	N/A	Intron Variant
KIAA0586 transcript variant 3	NM_001244191.2:c.3914-129… NM_001244191.2:c.3914-1299_3914-1298del	N/A	Intron Variant
KIAA0586 transcript variant 4	NM_001244192.2:c.4037-129… NM_001244192.2:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant 6	NM_001244193.2:c.3749-129… NM_001244193.2:c.3749-1299_3749-1298del	N/A	Intron Variant
KIAA0586 transcript variant 7	NM_001329943.3:c.4169-129… NM_001329943.3:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant 8	NM_001329944.2:c.4169-129… NM_001329944.2:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant 9	NM_001329945.2:c.3914-129… NM_001329945.2:c.3914-1299_3914-1298del	N/A	Intron Variant
KIAA0586 transcript variant 10	NM_001329946.2:c.4169-129… NM_001329946.2:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant 11	NM_001329947.2:c.4037-129… NM_001329947.2:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant 12	NM_001364700.1:c.3914-129… NM_001364700.1:c.3914-1299_3914-1298del	N/A	Intron Variant
KIAA0586 transcript variant 13	NM_001364701.2:c.3914-129… NM_001364701.2:c.3914-1299_3914-1298del	N/A	Intron Variant
KIAA0586 transcript variant 5	NM_014749.5:c.3941-1299_3… NM_014749.5:c.3941-1299_3941-1298del	N/A	Intron Variant
KIAA0586 transcript variant X1	XM_024449779.2:c.4292-129… XM_024449779.2:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X2	XM_024449780.2:c.4193-129… XM_024449780.2:c.4193-1299_4193-1298del	N/A	Intron Variant
KIAA0586 transcript variant X3	XM_024449781.2:c.4292-129… XM_024449781.2:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X19	XM_024449787.2:c.3773-129… XM_024449787.2:c.3773-1299_3773-1298del	N/A	Intron Variant
KIAA0586 transcript variant X21	XM_024449791.2:c.4193-129… XM_024449791.2:c.4193-1299_4193-1298del	N/A	Intron Variant
KIAA0586 transcript variant X4	XM_047432000.1:c.4292-129… XM_047432000.1:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X5	XM_047432001.1:c.4037-129… XM_047432001.1:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant X6	XM_047432002.1:c.4037-129… XM_047432002.1:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant X7	XM_047432003.1:c.4160-129… XM_047432003.1:c.4160-1299_4160-1298del	N/A	Intron Variant
KIAA0586 transcript variant X8	XM_047432004.1:c.4292-129… XM_047432004.1:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X9	XM_047432005.1:c.4292-129… XM_047432005.1:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X10	XM_047432006.1:c.4160-129… XM_047432006.1:c.4160-1299_4160-1298del	N/A	Intron Variant
KIAA0586 transcript variant X11	XM_047432007.1:c.4292-129… XM_047432007.1:c.4292-1299_4292-1298del	N/A	Intron Variant
KIAA0586 transcript variant X12	XM_047432008.1:c.4169-129… XM_047432008.1:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant X13	XM_047432009.1:c.4169-129… XM_047432009.1:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant X14	XM_047432010.1:c.4169-129… XM_047432010.1:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant X15	XM_047432011.1:c.4169-129… XM_047432011.1:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant X16	XM_047432012.1:c.4037-129… XM_047432012.1:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant X17	XM_047432013.1:c.4169-129… XM_047432013.1:c.4169-1299_4169-1298del	N/A	Intron Variant
KIAA0586 transcript variant X18	XM_047432014.1:c.4037-129… XM_047432014.1:c.4037-1299_4037-1298del	N/A	Intron Variant
KIAA0586 transcript variant X20	XM_047432015.1:c.4037-129… XM_047432015.1:c.4037-1299_4037-1298del	N/A	Intron Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	TGT=	delGT	dupGT
GRCh38.p14 chr 14	NC_000014.9:g.58507255_58507257=	NC_000014.9:g.58507256_58507257del	NC_000014.9:g.58507256_58507257dup
GRCh37.p13 chr 14	NC_000014.8:g.58973973_58973975=	NC_000014.8:g.58973974_58973975del	NC_000014.8:g.58973974_58973975dup
KIAA0586 RefSeqGene (LRG_1096)	NG_051335.2:g.84871_84873=	NG_051335.2:g.84872_84873del	NG_051335.2:g.84872_84873dup
KIAA0586 transcript variant 1	NM_001244189.1:c.4328-1300=	NM_001244189.1:c.4328-1299_4328-1298del	NM_001244189.1:c.4328-1299_4328-1298dup
KIAA0586 transcript variant 1	NM_001244189.2:c.4328-1300=	NM_001244189.2:c.4328-1299_4328-1298del	NM_001244189.2:c.4328-1299_4328-1298dup
KIAA0586 transcript variant 2	NM_001244190.1:c.4124-1300=	NM_001244190.1:c.4124-1299_4124-1298del	NM_001244190.1:c.4124-1299_4124-1298dup
KIAA0586 transcript variant 2	NM_001244190.2:c.4124-1300=	NM_001244190.2:c.4124-1299_4124-1298del	NM_001244190.2:c.4124-1299_4124-1298dup
KIAA0586 transcript variant 3	NM_001244191.1:c.3914-1300=	NM_001244191.1:c.3914-1299_3914-1298del	NM_001244191.1:c.3914-1299_3914-1298dup
KIAA0586 transcript variant 3	NM_001244191.2:c.3914-1300=	NM_001244191.2:c.3914-1299_3914-1298del	NM_001244191.2:c.3914-1299_3914-1298dup
KIAA0586 transcript variant 4	NM_001244192.1:c.4037-1300=	NM_001244192.1:c.4037-1299_4037-1298del	NM_001244192.1:c.4037-1299_4037-1298dup
KIAA0586 transcript variant 4	NM_001244192.2:c.4037-1300=	NM_001244192.2:c.4037-1299_4037-1298del	NM_001244192.2:c.4037-1299_4037-1298dup
KIAA0586 transcript variant 6	NM_001244193.1:c.3749-1300=	NM_001244193.1:c.3749-1299_3749-1298del	NM_001244193.1:c.3749-1299_3749-1298dup
KIAA0586 transcript variant 6	NM_001244193.2:c.3749-1300=	NM_001244193.2:c.3749-1299_3749-1298del	NM_001244193.2:c.3749-1299_3749-1298dup
KIAA0586 transcript variant 7	NM_001329943.3:c.4169-1300=	NM_001329943.3:c.4169-1299_4169-1298del	NM_001329943.3:c.4169-1299_4169-1298dup
KIAA0586 transcript variant 8	NM_001329944.2:c.4169-1300=	NM_001329944.2:c.4169-1299_4169-1298del	NM_001329944.2:c.4169-1299_4169-1298dup
KIAA0586 transcript variant 9	NM_001329945.2:c.3914-1300=	NM_001329945.2:c.3914-1299_3914-1298del	NM_001329945.2:c.3914-1299_3914-1298dup
KIAA0586 transcript variant 10	NM_001329946.2:c.4169-1300=	NM_001329946.2:c.4169-1299_4169-1298del	NM_001329946.2:c.4169-1299_4169-1298dup
KIAA0586 transcript variant 11	NM_001329947.2:c.4037-1300=	NM_001329947.2:c.4037-1299_4037-1298del	NM_001329947.2:c.4037-1299_4037-1298dup
KIAA0586 transcript variant 12	NM_001364700.1:c.3914-1300=	NM_001364700.1:c.3914-1299_3914-1298del	NM_001364700.1:c.3914-1299_3914-1298dup
KIAA0586 transcript variant 13	NM_001364701.2:c.3914-1300=	NM_001364701.2:c.3914-1299_3914-1298del	NM_001364701.2:c.3914-1299_3914-1298dup
KIAA0586 transcript variant 5	NM_014749.3:c.3941-1300=	NM_014749.3:c.3941-1299_3941-1298del	NM_014749.3:c.3941-1299_3941-1298dup
KIAA0586 transcript variant 5	NM_014749.5:c.3941-1300=	NM_014749.5:c.3941-1299_3941-1298del	NM_014749.5:c.3941-1299_3941-1298dup
KIAA0586 transcript variant X1	XM_005268242.1:c.3914-1300=	XM_005268242.1:c.3914-1299_3914-1298del	XM_005268242.1:c.3914-1299_3914-1298dup
KIAA0586 transcript variant X1	XM_024449779.2:c.4292-1300=	XM_024449779.2:c.4292-1299_4292-1298del	XM_024449779.2:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X2	XM_024449780.2:c.4193-1300=	XM_024449780.2:c.4193-1299_4193-1298del	XM_024449780.2:c.4193-1299_4193-1298dup
KIAA0586 transcript variant X3	XM_024449781.2:c.4292-1300=	XM_024449781.2:c.4292-1299_4292-1298del	XM_024449781.2:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X19	XM_024449787.2:c.3773-1300=	XM_024449787.2:c.3773-1299_3773-1298del	XM_024449787.2:c.3773-1299_3773-1298dup
KIAA0586 transcript variant X21	XM_024449791.2:c.4193-1300=	XM_024449791.2:c.4193-1299_4193-1298del	XM_024449791.2:c.4193-1299_4193-1298dup
KIAA0586 transcript variant X4	XM_047432000.1:c.4292-1300=	XM_047432000.1:c.4292-1299_4292-1298del	XM_047432000.1:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X5	XM_047432001.1:c.4037-1300=	XM_047432001.1:c.4037-1299_4037-1298del	XM_047432001.1:c.4037-1299_4037-1298dup
KIAA0586 transcript variant X6	XM_047432002.1:c.4037-1300=	XM_047432002.1:c.4037-1299_4037-1298del	XM_047432002.1:c.4037-1299_4037-1298dup
KIAA0586 transcript variant X7	XM_047432003.1:c.4160-1300=	XM_047432003.1:c.4160-1299_4160-1298del	XM_047432003.1:c.4160-1299_4160-1298dup
KIAA0586 transcript variant X8	XM_047432004.1:c.4292-1300=	XM_047432004.1:c.4292-1299_4292-1298del	XM_047432004.1:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X9	XM_047432005.1:c.4292-1300=	XM_047432005.1:c.4292-1299_4292-1298del	XM_047432005.1:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X10	XM_047432006.1:c.4160-1300=	XM_047432006.1:c.4160-1299_4160-1298del	XM_047432006.1:c.4160-1299_4160-1298dup
KIAA0586 transcript variant X11	XM_047432007.1:c.4292-1300=	XM_047432007.1:c.4292-1299_4292-1298del	XM_047432007.1:c.4292-1299_4292-1298dup
KIAA0586 transcript variant X12	XM_047432008.1:c.4169-1300=	XM_047432008.1:c.4169-1299_4169-1298del	XM_047432008.1:c.4169-1299_4169-1298dup
KIAA0586 transcript variant X13	XM_047432009.1:c.4169-1300=	XM_047432009.1:c.4169-1299_4169-1298del	XM_047432009.1:c.4169-1299_4169-1298dup
KIAA0586 transcript variant X14	XM_047432010.1:c.4169-1300=	XM_047432010.1:c.4169-1299_4169-1298del	XM_047432010.1:c.4169-1299_4169-1298dup
KIAA0586 transcript variant X15	XM_047432011.1:c.4169-1300=	XM_047432011.1:c.4169-1299_4169-1298del	XM_047432011.1:c.4169-1299_4169-1298dup
KIAA0586 transcript variant X16	XM_047432012.1:c.4037-1300=	XM_047432012.1:c.4037-1299_4037-1298del	XM_047432012.1:c.4037-1299_4037-1298dup
KIAA0586 transcript variant X17	XM_047432013.1:c.4169-1300=	XM_047432013.1:c.4169-1299_4169-1298del	XM_047432013.1:c.4169-1299_4169-1298dup
KIAA0586 transcript variant X18	XM_047432014.1:c.4037-1300=	XM_047432014.1:c.4037-1299_4037-1298del	XM_047432014.1:c.4037-1299_4037-1298dup
KIAA0586 transcript variant X20	XM_047432015.1:c.4037-1300=	XM_047432015.1:c.4037-1299_4037-1298del	XM_047432015.1:c.4037-1299_4037-1298dup

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

1 Frequency submission

No	Submitter	Submission ID	Date (Build)
1	ALFA	NC_000014.9 - 58507255	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID	History Updated (Build)
rs33947100	May 11, 2012 (137)
rs140037679	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
5244697823	NC_000014.9:58507254:TGT:T	NC_000014.9:58507254:TGT:T	(self)
5244697823	NC_000014.9:58507254:TGT:TGTGT	NC_000014.9:58507254:TGT:TGTGT	(self)

Removed from this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Destination RSIDs
ss3212441323	NC_000014.9:58507254::TG	NC_000014.9:58507254:TGT:TGTGT
ss3212441324	NC_000014.9:58507254:TG:	NC_000014.9:58507254:TGT:T

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1555398616

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1555398616