Name: rs777923330
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.

rs777923330

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:44129524-44129529 (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: delG / dupG
Variation Type: Indel Insertion and Deletion
Frequency: delG=0.000004 (1/264690, TOPMED)
dupG=0.000072 (18/250162, GnomAD_exome)
dupG=0.000092 (11/119908, ExAC) (+ 2 more)
delG=0.00000 (0/14050, ALFA)
dupG=0.00000 (0/14050, ALFA)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: KLF17 : Frameshift 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	14050	GGGGGG=1.00000	GGGGG=0.00000, GGGGGGG=0.00000	1.0	N/A
European	Sub	9690	GGGGGG=1.0000	GGGGG=0.0000, GGGGGGG=0.0000	1.0	N/A
African	Sub	2898	GGGGGG=1.0000	GGGGG=0.0000, GGGGGGG=0.0000	1.0	N/A
African Others	Sub	114	GGGGGG=1.000	GGGGG=0.000, GGGGGGG=0.000	1.0	N/A
African American	Sub	2784	GGGGGG=1.0000	GGGGG=0.0000, GGGGGGG=0.0000	1.0	N/A
Asian	Sub	112	GGGGGG=1.000	GGGGG=0.000, GGGGGGG=0.000	1.0	N/A
East Asian	Sub	86	GGGGGG=1.00	GGGGG=0.00, GGGGGGG=0.00	1.0	N/A
Other Asian	Sub	26	GGGGGG=1.00	GGGGG=0.00, GGGGGGG=0.00	1.0	N/A
Latin American 1	Sub	146	GGGGGG=1.000	GGGGG=0.000, GGGGGGG=0.000	1.0	N/A
Latin American 2	Sub	610	GGGGGG=1.000	GGGGG=0.000, GGGGGGG=0.000	1.0	N/A
South Asian	Sub	98	GGGGGG=1.00	GGGGG=0.00, GGGGGGG=0.00	1.0	N/A
Other	Sub	496	GGGGGG=1.000	GGGGG=0.000, GGGGGGG=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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	(G)₆=0.999996	delG=0.000004
gnomAD - Exomes	Global	Study-wide	250162	- No frequency provided	dupG=0.000072
gnomAD - Exomes	European	Sub	134614	- No frequency provided	dupG=0.000007
gnomAD - Exomes	Asian	Sub	48792	- No frequency provided	dupG=0.00033
gnomAD - Exomes	American	Sub	34436	- No frequency provided	dupG=0.00000
gnomAD - Exomes	African	Sub	16252	- No frequency provided	dupG=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9978	- No frequency provided	dupG=0.0000
gnomAD - Exomes	Other	Sub	6090	- No frequency provided	dupG=0.0002
ExAC	Global	Study-wide	119908	- No frequency provided	dupG=0.000092
ExAC	Europe	Sub	72910	- No frequency provided	dupG=0.00000
ExAC	Asian	Sub	24138	- No frequency provided	dupG=0.00046
ExAC	American	Sub	11570	- No frequency provided	dupG=0.00000
ExAC	African	Sub	10394	- No frequency provided	dupG=0.00000
ExAC	Other	Sub	896	- No frequency provided	dupG=0.000
Allele Frequency Aggregator	Total	Global	14050	(G)₆=1.00000	delG=0.00000, dupG=0.00000
Allele Frequency Aggregator	European	Sub	9690	(G)₆=1.0000	delG=0.0000, dupG=0.0000
Allele Frequency Aggregator	African	Sub	2898	(G)₆=1.0000	delG=0.0000, dupG=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	(G)₆=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Other	Sub	496	(G)₆=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	(G)₆=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	Asian	Sub	112	(G)₆=1.000	delG=0.000, dupG=0.000
Allele Frequency Aggregator	South Asian	Sub	98	(G)₆=1.00	delG=0.00, dupG=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 1	NC_000001.11:g.44129529del
GRCh38.p14 chr 1	NC_000001.11:g.44129529dup
GRCh37.p13 chr 1	NC_000001.10:g.44595201del
GRCh37.p13 chr 1	NC_000001.10:g.44595201dup

Gene: KLF17, Kruppel like factor 17 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KLF17 transcript	NM_173484.4:c.258del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17	NP_775755.3:p.Pro87fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript	NM_173484.4:c.258dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17	NP_775755.3:p.Pro87fs	P (Pro) > A (Ala)	Frameshift Variant
KLF17 transcript variant X1	XM_047445936.1:c.147del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_047301892.1:p.Pro50fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript variant X1	XM_047445936.1:c.147dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_047301892.1:p.Pro50fs	P (Pro) > A (Ala)	Frameshift Variant
KLF17 transcript variant X2	XM_011540700.2:c.147del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_011539002.1:p.Pro50fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript variant X2	XM_011540700.2:c.147dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_011539002.1:p.Pro50fs	P (Pro) > A (Ala)	Frameshift Variant
KLF17 transcript variant X3	XM_047445938.1:c.147del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_047301894.1:p.Pro50fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript variant X3	XM_047445938.1:c.147dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17 isoform X1	XP_047301894.1:p.Pro50fs	P (Pro) > A (Ala)	Frameshift Variant
KLF17 transcript variant X4	XM_005270465.4:c.339del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17 isoform X2	XP_005270522.2:p.Pro114fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript variant X4	XM_005270465.4:c.339dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17 isoform X2	XP_005270522.2:p.Pro114fs	P (Pro) > A (Ala)	Frameshift Variant
KLF17 transcript variant X5	XM_011540704.3:c.339del	G [GGG] > G [GG]	Coding Sequence Variant
Krueppel-like factor 17 isoform X3	XP_011539006.1:p.Pro114fs	G (Gly) > G (Gly)	Frameshift Variant
KLF17 transcript variant X5	XM_011540704.3:c.339dup	P [CCA] > A [GCCA]	Coding Sequence Variant
Krueppel-like factor 17 isoform X3	XP_011539006.1:p.Pro114fs	P (Pro) > A (Ala)	Frameshift 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	(G)₆=	delG	dupG
GRCh38.p14 chr 1	NC_000001.11:g.44129524_44129529=	NC_000001.11:g.44129529del	NC_000001.11:g.44129529dup
GRCh37.p13 chr 1	NC_000001.10:g.44595196_44595201=	NC_000001.10:g.44595201del	NC_000001.10:g.44595201dup
KLF17 transcript	NM_173484.4:c.253_258=	NM_173484.4:c.258del	NM_173484.4:c.258dup
KLF17 transcript	NM_173484.3:c.253_258=	NM_173484.3:c.258del	NM_173484.3:c.258dup
KLF17 transcript variant X4	XM_005270465.4:c.334_339=	XM_005270465.4:c.339del	XM_005270465.4:c.339dup
KLF17 transcript variant X2	XM_005270465.3:c.334_339=	XM_005270465.3:c.339del	XM_005270465.3:c.339dup
KLF17 transcript variant X5	XM_005270465.2:c.334_339=	XM_005270465.2:c.339del	XM_005270465.2:c.339dup
KLF17 transcript variant X2	XM_005270465.1:c.253_258=	XM_005270465.1:c.258del	XM_005270465.1:c.258dup
KLF17 transcript variant X5	XM_011540704.3:c.334_339=	XM_011540704.3:c.339del	XM_011540704.3:c.339dup
KLF17 transcript variant X3	XM_011540704.2:c.334_339=	XM_011540704.2:c.339del	XM_011540704.2:c.339dup
KLF17 transcript variant X6	XM_011540704.1:c.334_339=	XM_011540704.1:c.339del	XM_011540704.1:c.339dup
KLF17 transcript variant X2	XM_011540700.2:c.142_147=	XM_011540700.2:c.147del	XM_011540700.2:c.147dup
KLF17 transcript variant X1	XM_011540700.1:c.142_147=	XM_011540700.1:c.147del	XM_011540700.1:c.147dup
KLF17 transcript variant X1	XM_047445936.1:c.142_147=	XM_047445936.1:c.147del	XM_047445936.1:c.147dup
KLF17 transcript variant X3	XM_047445938.1:c.142_147=	XM_047445938.1:c.147del	XM_047445938.1:c.147dup
Krueppel-like factor 17	NP_775755.3:p.Gly85_Gly86=	NP_775755.3:p.Pro87fs	NP_775755.3:p.Pro87fs
Krueppel-like factor 17 isoform X2	XP_005270522.2:p.Gly112_Gly113=	XP_005270522.2:p.Pro114fs	XP_005270522.2:p.Pro114fs
Krueppel-like factor 17 isoform X3	XP_011539006.1:p.Gly112_Gly113=	XP_011539006.1:p.Pro114fs	XP_011539006.1:p.Pro114fs
Krueppel-like factor 17 isoform X1	XP_011539002.1:p.Gly48_Gly49=	XP_011539002.1:p.Pro50fs	XP_011539002.1:p.Pro50fs
Krueppel-like factor 17 isoform X1	XP_047301892.1:p.Gly48_Gly49=	XP_047301892.1:p.Pro50fs	XP_047301892.1:p.Pro50fs
Krueppel-like factor 17 isoform X1	XP_047301894.1:p.Gly48_Gly49=	XP_047301894.1:p.Pro50fs	XP_047301894.1:p.Pro50fs
Krueppel-like factor 17 isoform X2	XP_005270522.1:p.Gly85_Gly86=	XP_005270522.1:p.Pro87fs	XP_005270522.1:p.Pro87fs

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#.

6 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_EXAC	ss1711615218	Apr 01, 2015 (144)
2	GNOMAD	ss2731446019	Nov 08, 2017 (151)
3	FSA-LAB	ss3983929579	Apr 27, 2021 (155)
4	GNOMAD	ss3992374816	Apr 27, 2021 (155)
5	GNOMAD	ss3992374817	Apr 27, 2021 (155)
6	TOPMED	ss4447142742	Apr 27, 2021 (155)
7	ExAC	NC_000001.10 - 44595196	Oct 11, 2018 (152)
8	gnomAD - Genomes Submission ignored due to conflicting rows: Row 9260556 (NC_000001.11:44129523::G 1/140160) Row 9260557 (NC_000001.11:44129523:G: 1/140160)	-	Apr 27, 2021 (155)
9	gnomAD - Genomes Submission ignored due to conflicting rows: Row 9260556 (NC_000001.11:44129523::G 1/140160) Row 9260557 (NC_000001.11:44129523:G: 1/140160)	-	Apr 27, 2021 (155)
10	gnomAD - Exomes	NC_000001.10 - 44595196	Jul 12, 2019 (153)
11	TopMed	NC_000001.11 - 44129524	Apr 27, 2021 (155)
12	ALFA	NC_000001.11 - 44129524	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
10749077, ss3992374817, ss4447142742	NC_000001.11:44129523:G:	NC_000001.11:44129523:GGGGGG:GGGGG	(self)
7133388684	NC_000001.11:44129523:GGGGGG:GGGGG	NC_000001.11:44129523:GGGGGG:GGGGG	(self)
4708754, 462595, ss1711615218, ss2731446019, ss3983929579	NC_000001.10:44595195::G	NC_000001.11:44129523:GGGGGG:GGGGG… NC_000001.11:44129523:GGGGGG:GGGGGGG	(self)
ss3992374816	NC_000001.11:44129523::G	NC_000001.11:44129523:GGGGGG:GGGGG… NC_000001.11:44129523:GGGGGG:GGGGGGG	(self)
7133388684	NC_000001.11:44129523:GGGGGG:GGGGG… NC_000001.11:44129523:GGGGGG:GGGGGGG	NC_000001.11:44129523:GGGGGG:GGGGG… NC_000001.11:44129523:GGGGGG:GGGGGGG	(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 rs777923330

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
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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

rs777923330