Name: rs1488764763
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.

rs1488764763

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:178209087 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.00000 (0/14050, ALFA)
C=0.00000 (0/14050, ALFA)
A=0.0003 (1/2922, KOREAN) (+ 1 more)
A=0.0011 (2/1832, Korea1K)

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

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
Allele Frequency Aggregator	Total	Global	14050	G=1.00000	A=0.00000, C=0.00000
Allele Frequency Aggregator	European	Sub	9690	G=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	African	Sub	2898	G=1.0000	A=0.0000, C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Other	Sub	496	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Asian	Sub	112	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	G=1.00	A=0.00, C=0.00
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9997	A=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9989	A=0.0011

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 5	NC_000005.10:g.178209087G>A
GRCh38.p14 chr 5	NC_000005.10:g.178209087G>C
GRCh37.p13 chr 5	NC_000005.9:g.177636088G>A
GRCh37.p13 chr 5	NC_000005.9:g.177636088G>C
PHYKPL RefSeqGene	NG_033253.2:g.28736C>T
PHYKPL RefSeqGene	NG_033253.2:g.28736C>G

Gene: PHYKPL, 5-phosphohydroxy-L-lysine phospho-lyase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHYKPL transcript variant 3	NM_001278346.1:c.32-172C… NM_001278346.1:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant 2	NM_153373.4:c.*32-172C>T	N/A	Intron Variant
PHYKPL transcript variant 1	NR_103508.1:n.	N/A	Intron Variant
PHYKPL transcript variant 4	NR_103509.1:n.	N/A	Intron Variant
PHYKPL transcript variant 5	NR_103510.1:n.	N/A	Intron Variant
PHYKPL transcript variant X10	XM_006714925.3:c.32-172C… XM_006714925.3:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X1	XM_011534669.3:c.32-172C… XM_011534669.3:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X4	XM_011534670.4:c.32-172C… XM_011534670.4:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X5	XM_011534671.3:c.32-172C… XM_011534671.3:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X17	XM_011534674.3:c.32-172C… XM_011534674.3:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X14	XM_024446240.2:c.32-172C… XM_024446240.2:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X23	XM_024446243.2:c.32-172C… XM_024446243.2:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X24	XM_024446245.2:c.32-172C… XM_024446245.2:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X25	XM_024446247.2:c.32-172C… XM_024446247.2:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X27	XM_024446250.2:c.32-172C… XM_024446250.2:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X8	XM_047417837.1:c.32-172C… XM_047417837.1:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X15	XM_047417838.1:c.32-172C… XM_047417838.1:c.32-172C>T	N/A	Intron Variant
PHYKPL transcript variant X7	XM_017009995.2:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X19	XM_024446241.2:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X28	XM_024446251.2:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X29	XM_024446252.2:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X18	XM_047417839.1:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X20	XM_047417840.1:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X22	XM_047417841.1:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X30	XM_047417843.1:c.	N/A	Genic Downstream Transcript Variant
PHYKPL transcript variant X9	XR_002956187.2:n.	N/A	Intron Variant
PHYKPL transcript variant X11	XR_002956188.2:n.	N/A	Intron Variant
PHYKPL transcript variant X16	XR_002956189.2:n.	N/A	Intron Variant
PHYKPL transcript variant X2	XR_007058648.1:n.	N/A	Intron Variant
PHYKPL transcript variant X3	XR_007058649.1:n.	N/A	Intron Variant
PHYKPL transcript variant X6	XR_007058650.1:n.	N/A	Intron Variant
PHYKPL transcript variant X12	XR_007058651.1:n.	N/A	Intron Variant
PHYKPL transcript variant X13	XR_007058652.1:n.	N/A	Intron Variant
PHYKPL transcript variant X21	XR_007058653.1:n.	N/A	Intron Variant
PHYKPL transcript variant X26	XR_007058654.1:n.	N/A	Intron Variant

Gene: HNRNPAB, heterogeneous nuclear ribonucleoprotein A/B (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HNRNPAB transcript variant 2	NM_004499.4:c.670-243G>A	N/A	Intron Variant
HNRNPAB transcript variant 1	NM_031266.3:c.670-243G>A	N/A	Intron Variant
HNRNPAB transcript variant X1	XM_047417138.1:c.670-243G… XM_047417138.1:c.670-243G>A	N/A	Intron Variant
HNRNPAB transcript variant X2	XM_047417139.1:c.670-243G… XM_047417139.1:c.670-243G>A	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	G=	A	C
GRCh38.p14 chr 5	NC_000005.10:g.178209087=	NC_000005.10:g.178209087G>A	NC_000005.10:g.178209087G>C
GRCh37.p13 chr 5	NC_000005.9:g.177636088=	NC_000005.9:g.177636088G>A	NC_000005.9:g.177636088G>C
PHYKPL RefSeqGene	NG_033253.2:g.28736=	NG_033253.2:g.28736C>T	NG_033253.2:g.28736C>G
PHYKPL transcript variant 3	NM_001278346.1:c.*32-172=	NM_001278346.1:c.*32-172C>T	NM_001278346.1:c.*32-172C>G
HNRNPAB transcript variant 2	NM_004499.3:c.670-243=	NM_004499.3:c.670-243G>A	NM_004499.3:c.670-243G>C
HNRNPAB transcript variant 2	NM_004499.4:c.670-243=	NM_004499.4:c.670-243G>A	NM_004499.4:c.670-243G>C
HNRNPAB transcript variant 1	NM_031266.2:c.670-243=	NM_031266.2:c.670-243G>A	NM_031266.2:c.670-243G>C
HNRNPAB transcript variant 1	NM_031266.3:c.670-243=	NM_031266.3:c.670-243G>A	NM_031266.3:c.670-243G>C
PHYKPL transcript variant 2	NM_153373.3:c.*32-172=	NM_153373.3:c.*32-172C>T	NM_153373.3:c.*32-172C>G
PHYKPL transcript variant 2	NM_153373.4:c.*32-172=	NM_153373.4:c.*32-172C>T	NM_153373.4:c.*32-172C>G
PHYKPL transcript variant X1	XM_005266001.1:c.*32-172=	XM_005266001.1:c.*32-172C>T	XM_005266001.1:c.*32-172C>G
PHYKPL transcript variant X17	XM_005266002.1:c.*32-172=	XM_005266002.1:c.*32-172C>T	XM_005266002.1:c.*32-172C>G
PHYKPL transcript variant X10	XM_006714925.3:c.*32-172=	XM_006714925.3:c.*32-172C>T	XM_006714925.3:c.*32-172C>G
PHYKPL transcript variant X1	XM_011534669.3:c.*32-172=	XM_011534669.3:c.*32-172C>T	XM_011534669.3:c.*32-172C>G
PHYKPL transcript variant X4	XM_011534670.4:c.*32-172=	XM_011534670.4:c.*32-172C>T	XM_011534670.4:c.*32-172C>G
PHYKPL transcript variant X5	XM_011534671.3:c.*32-172=	XM_011534671.3:c.*32-172C>T	XM_011534671.3:c.*32-172C>G
PHYKPL transcript variant X17	XM_011534674.3:c.*32-172=	XM_011534674.3:c.*32-172C>T	XM_011534674.3:c.*32-172C>G
PHYKPL transcript variant X14	XM_024446240.2:c.*32-172=	XM_024446240.2:c.*32-172C>T	XM_024446240.2:c.*32-172C>G
PHYKPL transcript variant X23	XM_024446243.2:c.*32-172=	XM_024446243.2:c.*32-172C>T	XM_024446243.2:c.*32-172C>G
PHYKPL transcript variant X24	XM_024446245.2:c.*32-172=	XM_024446245.2:c.*32-172C>T	XM_024446245.2:c.*32-172C>G
PHYKPL transcript variant X25	XM_024446247.2:c.*32-172=	XM_024446247.2:c.*32-172C>T	XM_024446247.2:c.*32-172C>G
PHYKPL transcript variant X27	XM_024446250.2:c.*32-172=	XM_024446250.2:c.*32-172C>T	XM_024446250.2:c.*32-172C>G
HNRNPAB transcript variant X1	XM_047417138.1:c.670-243=	XM_047417138.1:c.670-243G>A	XM_047417138.1:c.670-243G>C
HNRNPAB transcript variant X2	XM_047417139.1:c.670-243=	XM_047417139.1:c.670-243G>A	XM_047417139.1:c.670-243G>C
PHYKPL transcript variant X8	XM_047417837.1:c.*32-172=	XM_047417837.1:c.*32-172C>T	XM_047417837.1:c.*32-172C>G
PHYKPL transcript variant X15	XM_047417838.1:c.*32-172=	XM_047417838.1:c.*32-172C>T	XM_047417838.1:c.*32-172C>G

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#.

4 SubSNP, 5 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KRGDB	ss3910394974	Apr 26, 2020 (154)
2	KOGIC	ss3958274832	Apr 26, 2020 (154)
3	TOPMED	ss4690091876	Apr 26, 2021 (155)
4	TOPMED	ss4690091877	Apr 26, 2021 (155)
5	KOREAN population from KRGDB	NC_000005.9 - 177636088	Apr 26, 2020 (154)
6	Korean Genome Project	NC_000005.10 - 178209087	Apr 26, 2020 (154)
7	TopMed Submission ignored due to conflicting rows: Row 527469433 (NC_000005.10:178209086:G:A 1/264690) Row 527469434 (NC_000005.10:178209086:G:C 2/264690)	-	Apr 26, 2021 (155)
8	TopMed Submission ignored due to conflicting rows: Row 527469433 (NC_000005.10:178209086:G:A 1/264690) Row 527469434 (NC_000005.10:178209086:G:C 2/264690)	-	Apr 26, 2021 (155)
9	ALFA	NC_000005.10 - 178209087	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
17572368, ss3910394974	NC_000005.9:177636087:G:A	NC_000005.10:178209086:G:A	(self)
14652833, 13722332043, ss3958274832, ss4690091876	NC_000005.10:178209086:G:A	NC_000005.10:178209086:G:A	(self)
13722332043, ss4690091877	NC_000005.10:178209086:G:C	NC_000005.10:178209086:G:C	(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 rs1488764763

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

rs1488764763