Name: rs1491565585
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.

rs1491565585

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:9823423-9823424 (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: insTA
Variation Type: Insertion
Frequency: insTA=0.000159 (22/138166, GnomAD)
insTA=0.00008 (1/11862, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ARPC4-TTLL3 : Intron Variant
TTLL3 : 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	HTRZ	HWEP
Total	Global	11862	=0.99992	TA=0.00008	0.999831	0.000169	0
European	Sub	7618	=1.0000	TA=0.0000	1.0	0.0	N/A
African	Sub	2816	=0.9996	TA=0.0004	0.99929	0.00071	0
African Others	Sub	108	=1.000	TA=0.000	1.0	0.0	N/A
African American	Sub	2708	=0.9996	TA=0.0004	0.999261	0.000739	0
Asian	Sub	108	=1.000	TA=0.000	1.0	0.0	N/A
East Asian	Sub	84	=1.00	TA=0.00	1.0	0.0	N/A
Other Asian	Sub	24	=1.00	TA=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	=1.000	TA=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	=1.000	TA=0.000	1.0	0.0	N/A
South Asian	Sub	94	=1.00	TA=0.00	1.0	0.0	N/A
Other	Sub	470	=1.000	TA=0.000	1.0	0.0	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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
gnomAD - Genomes	Global	Study-wide	138166	- No frequency provided	insTA=0.000159
gnomAD - Genomes	European	Sub	74730	- No frequency provided	insTA=0.00003
gnomAD - Genomes	African	Sub	41444	- No frequency provided	insTA=0.00048
gnomAD - Genomes	American	Sub	13446	- No frequency provided	insTA=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	- No frequency provided	insTA=0.0000
gnomAD - Genomes	East Asian	Sub	3108	- No frequency provided	insTA=0.0000
gnomAD - Genomes	Other	Sub	2122	- No frequency provided	insTA=0.0000
Allele Frequency Aggregator	Total	Global	11862	- No frequency provided	insTA=0.00008
Allele Frequency Aggregator	European	Sub	7618	- No frequency provided	insTA=0.0000
Allele Frequency Aggregator	African	Sub	2816	- No frequency provided	insTA=0.0004
Allele Frequency Aggregator	Latin American 2	Sub	610	- No frequency provided	insTA=0.000
Allele Frequency Aggregator	Other	Sub	470	- No frequency provided	insTA=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	- No frequency provided	insTA=0.000
Allele Frequency Aggregator	Asian	Sub	108	- No frequency provided	insTA=0.000
Allele Frequency Aggregator	South Asian	Sub	94	- No frequency provided	insTA=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 3	NC_000003.12:g.9823423_9823424insTA
GRCh37.p13 chr 3	NC_000003.11:g.9865107_9865108insTA

Gene: TTLL3, tubulin tyrosine ligase like 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TTLL3 transcript variant 1	NM_001025930.5:c.1155-237… NM_001025930.5:c.1155-2377_1155-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 3	NM_001366051.2:c.726-2377… NM_001366051.2:c.726-2377_726-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 4	NM_001387446.1:c.855-2377… NM_001387446.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 5	NM_001387447.1:c.855-2377… NM_001387447.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 6	NM_001387448.1:c.726-2377… NM_001387448.1:c.726-2377_726-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 7	NM_001387449.1:c.726-2377… NM_001387449.1:c.726-2377_726-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 8	NM_001387450.1:c.900-2377… NM_001387450.1:c.900-2377_900-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 9	NM_001387451.1:c.756-2377… NM_001387451.1:c.756-2377_756-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 10	NM_001387452.1:c.627-2377… NM_001387452.1:c.627-2377_627-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 11	NM_001387453.1:c.627-2377… NM_001387453.1:c.627-2377_627-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 12	NM_001387454.1:c.855-2377… NM_001387454.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 13	NM_001387455.1:c.855-2377… NM_001387455.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 14	NM_001387456.1:c.855-2377… NM_001387456.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 15	NM_001387457.1:c.855-2377… NM_001387457.1:c.855-2377_855-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 16	NM_001387458.1:c.627-2377… NM_001387458.1:c.627-2377_627-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 17	NM_001387459.1:c.756-2377… NM_001387459.1:c.756-2377_756-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 31	NM_001387460.1:c.756-2377… NM_001387460.1:c.756-2377_756-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 19	NM_001387461.1:c.726-2377… NM_001387461.1:c.726-2377_726-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 20	NM_001387462.1:c.723-2377… NM_001387462.1:c.723-2377_723-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 21	NM_001387463.1:c.627-2377… NM_001387463.1:c.627-2377_627-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 22	NM_001387464.1:c.756-2377… NM_001387464.1:c.756-2377_756-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 23	NM_001387465.1:c.756-2377… NM_001387465.1:c.756-2377_756-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 24	NM_001387466.1:c.511+2682… NM_001387466.1:c.511+2682_511+2683insTA	N/A	Intron Variant
TTLL3 transcript variant 25	NM_001387467.1:c.90-2377_… NM_001387467.1:c.90-2377_90-2376insTA	N/A	Intron Variant
TTLL3 transcript variant 2	NR_037162.2:n.	N/A	Intron Variant
TTLL3 transcript variant 26	NR_170661.1:n.	N/A	Intron Variant
TTLL3 transcript variant 27	NR_170662.1:n.	N/A	Intron Variant
TTLL3 transcript variant 28	NR_170663.1:n.	N/A	Intron Variant
TTLL3 transcript variant 29	NR_170664.1:n.	N/A	Intron Variant
TTLL3 transcript variant 30	NR_170665.1:n.	N/A	Intron Variant

Gene: ARPC4-TTLL3, ARPC4-TTLL3 readthrough (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ARPC4-TTLL3 transcript	NM_001198793.1:c.909-2377… NM_001198793.1:c.909-2377_909-2376insTA	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	=	insTA
GRCh38.p14 chr 3	NC_000003.12:g.9823423_9823424=	NC_000003.12:g.9823423_9823424insTA
GRCh37.p13 chr 3	NC_000003.11:g.9865107_9865108=	NC_000003.11:g.9865107_9865108insTA
TTLL3 transcript variant 1	NM_001025930.3:c.1155-2376=	NM_001025930.3:c.1155-2377_1155-2376insTA
TTLL3 transcript variant 1	NM_001025930.5:c.1155-2376=	NM_001025930.5:c.1155-2377_1155-2376insTA
ARPC4-TTLL3 transcript	NM_001198793.1:c.909-2376=	NM_001198793.1:c.909-2377_909-2376insTA
TTLL3 transcript variant 3	NM_001366051.2:c.726-2376=	NM_001366051.2:c.726-2377_726-2376insTA
TTLL3 transcript variant 4	NM_001387446.1:c.855-2376=	NM_001387446.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 5	NM_001387447.1:c.855-2376=	NM_001387447.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 6	NM_001387448.1:c.726-2376=	NM_001387448.1:c.726-2377_726-2376insTA
TTLL3 transcript variant 7	NM_001387449.1:c.726-2376=	NM_001387449.1:c.726-2377_726-2376insTA
TTLL3 transcript variant 8	NM_001387450.1:c.900-2376=	NM_001387450.1:c.900-2377_900-2376insTA
TTLL3 transcript variant 9	NM_001387451.1:c.756-2376=	NM_001387451.1:c.756-2377_756-2376insTA
TTLL3 transcript variant 10	NM_001387452.1:c.627-2376=	NM_001387452.1:c.627-2377_627-2376insTA
TTLL3 transcript variant 11	NM_001387453.1:c.627-2376=	NM_001387453.1:c.627-2377_627-2376insTA
TTLL3 transcript variant 12	NM_001387454.1:c.855-2376=	NM_001387454.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 13	NM_001387455.1:c.855-2376=	NM_001387455.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 14	NM_001387456.1:c.855-2376=	NM_001387456.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 15	NM_001387457.1:c.855-2376=	NM_001387457.1:c.855-2377_855-2376insTA
TTLL3 transcript variant 16	NM_001387458.1:c.627-2376=	NM_001387458.1:c.627-2377_627-2376insTA
TTLL3 transcript variant 17	NM_001387459.1:c.756-2376=	NM_001387459.1:c.756-2377_756-2376insTA
TTLL3 transcript variant 31	NM_001387460.1:c.756-2376=	NM_001387460.1:c.756-2377_756-2376insTA
TTLL3 transcript variant 19	NM_001387461.1:c.726-2376=	NM_001387461.1:c.726-2377_726-2376insTA
TTLL3 transcript variant 20	NM_001387462.1:c.723-2376=	NM_001387462.1:c.723-2377_723-2376insTA
TTLL3 transcript variant 21	NM_001387463.1:c.627-2376=	NM_001387463.1:c.627-2377_627-2376insTA
TTLL3 transcript variant 22	NM_001387464.1:c.756-2376=	NM_001387464.1:c.756-2377_756-2376insTA
TTLL3 transcript variant 23	NM_001387465.1:c.756-2376=	NM_001387465.1:c.756-2377_756-2376insTA
TTLL3 transcript variant 24	NM_001387466.1:c.511+2683=	NM_001387466.1:c.511+2682_511+2683insTA
TTLL3 transcript variant 25	NM_001387467.1:c.90-2376=	NM_001387467.1:c.90-2377_90-2376insTA
TTLL3 transcript variant X1	XM_005265046.1:c.1284-2376=	XM_005265046.1:c.1284-2377_1284-2376insTA
TTLL3 transcript variant X2	XM_005265047.1:c.1185-2376=	XM_005265047.1:c.1185-2377_1185-2376insTA
TTLL3 transcript variant X3	XM_005265048.1:c.1284-2376=	XM_005265048.1:c.1284-2377_1284-2376insTA
TTLL3 transcript variant X4	XM_005265049.1:c.1284-2376=	XM_005265049.1:c.1284-2377_1284-2376insTA
TTLL3 transcript variant X5	XM_005265050.1:c.1284-2376=	XM_005265050.1:c.1284-2377_1284-2376insTA
TTLL3 transcript variant X6	XM_005265051.1:c.1284-2376=	XM_005265051.1:c.1284-2377_1284-2376insTA
TTLL3 transcript variant X7	XM_005265052.1:c.136+2683=	XM_005265052.1:c.136+2682_136+2683insTA
TTLL3 transcript variant X8	XM_005265053.1:c.136+2683=	XM_005265053.1:c.136+2682_136+2683insTA
TTLL3 transcript variant X9	XM_005265054.1:c.136+2683=	XM_005265054.1:c.136+2682_136+2683insTA
TTLL3 transcript variant X10	XM_005265055.1:c.136+2683=	XM_005265055.1:c.136+2682_136+2683insTA
TTLL3 transcript variant X11	XM_005265056.1:c.136+2683=	XM_005265056.1:c.136+2682_136+2683insTA

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 SubSNP, 2 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GNOMAD	ss4065663328	Apr 27, 2021 (155)
2	gnomAD - Genomes	NC_000003.12 - 9823424	Apr 27, 2021 (155)
3	ALFA	NC_000003.12 - 9823424	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
98715546, 5603075610, ss4065663328	NC_000003.12:9823423::TA	NC_000003.12:9823423::TA	(self)

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

No publications for rs1491565585

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1491565585