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dbSNP Short Genetic Variations

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.

rs375417190

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:3532408 (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=0.000125 (33/264690, TOPMED)
A=0.000121 (17/140246, GnomAD)
A=0.00036 (28/78560, PAGE_STUDY) (+ 3 more)
A=0.00008 (2/25004, ExAC)
A=0.00017 (4/23690, ALFA)
A=0.00008 (1/12758, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LRPAP1 : Missense 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 23690 G=0.99983 A=0.00017
European Sub 15824 G=1.00000 A=0.00000
African Sub 3924 G=0.9992 A=0.0008
African Others Sub 122 G=1.000 A=0.000
African American Sub 3802 G=0.9992 A=0.0008
Asian Sub 202 G=1.000 A=0.000
East Asian Sub 146 G=1.000 A=0.000
Other Asian Sub 56 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 2880 G=0.9997 A=0.0003


Help

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
TopMed Global Study-wide 264690 G=0.999875 A=0.000125
gnomAD - Genomes Global Study-wide 140246 G=0.999879 A=0.000121
gnomAD - Genomes European Sub 75940 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 42028 G=0.99962 A=0.00038
gnomAD - Genomes American Sub 13668 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
The PAGE Study Global Study-wide 78560 G=0.99964 A=0.00036
The PAGE Study AfricanAmerican Sub 32400 G=0.99938 A=0.00062
The PAGE Study Mexican Sub 10804 G=0.99954 A=0.00046
The PAGE Study Asian Sub 8310 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7914 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4526 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 G=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9990 A=0.0010
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
ExAC Global Study-wide 25004 G=0.99992 A=0.00008
ExAC Europe Sub 11218 G=1.00000 A=0.00000
ExAC Asian Sub 9974 G=1.0000 A=0.0000
ExAC African Sub 2038 G=0.9990 A=0.0010
ExAC American Sub 1574 G=1.0000 A=0.0000
ExAC Other Sub 200 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 23690 G=0.99983 A=0.00017
Allele Frequency Aggregator European Sub 15824 G=1.00000 A=0.00000
Allele Frequency Aggregator African Sub 3924 G=0.9992 A=0.0008
Allele Frequency Aggregator Other Sub 2880 G=0.9997 A=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 202 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 12758 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8482 G=1.0000 A=0.0000
GO Exome Sequencing Project African American Sub 4276 G=0.9998 A=0.0002
Help

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 4 NC_000004.12:g.3532408G>A
GRCh38.p14 chr 4 NC_000004.12:g.3532408G>C
GRCh37.p13 chr 4 NC_000004.11:g.3534135G>A
GRCh37.p13 chr 4 NC_000004.11:g.3534135G>C
LRPAP1 RefSeqGene (LRG_1299) NG_033873.1:g.5090C>T
LRPAP1 RefSeqGene (LRG_1299) NG_033873.1:g.5090C>G
Gene: LRPAP1, LDL receptor related protein associated protein 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LRPAP1 transcript variant 1 NM_002337.4:c.5C>T A [GCG] > V [GTG] Coding Sequence Variant
alpha-2-macroglobulin receptor-associated protein precursor NP_002328.1:p.Ala2Val A (Ala) > V (Val) Missense Variant
LRPAP1 transcript variant 1 NM_002337.4:c.5C>G A [GCG] > G [GGG] Coding Sequence Variant
alpha-2-macroglobulin receptor-associated protein precursor NP_002328.1:p.Ala2Gly A (Ala) > G (Gly) Missense Variant
LRPAP1 transcript variant 2 NR_110005.2:n. N/A Genic Upstream Transcript Variant
Help

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
Help

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 4 NC_000004.12:g.3532408= NC_000004.12:g.3532408G>A NC_000004.12:g.3532408G>C
GRCh37.p13 chr 4 NC_000004.11:g.3534135= NC_000004.11:g.3534135G>A NC_000004.11:g.3534135G>C
LRPAP1 RefSeqGene (LRG_1299) NG_033873.1:g.5090= NG_033873.1:g.5090C>T NG_033873.1:g.5090C>G
LRPAP1 transcript variant 1 NM_002337.4:c.5= NM_002337.4:c.5C>T NM_002337.4:c.5C>G
LRPAP1 transcript variant 1 NM_002337.3:c.5= NM_002337.3:c.5C>T NM_002337.3:c.5C>G
alpha-2-macroglobulin receptor-associated protein precursor NP_002328.1:p.Ala2= NP_002328.1:p.Ala2Val NP_002328.1:p.Ala2Gly
Help

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#.

12 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss712580558 Apr 25, 2013 (138)
2 EVA_EXAC ss1687408114 Apr 01, 2015 (144)
3 ILLUMINA ss1958652411 Feb 12, 2016 (147)
4 GNOMAD ss2734374759 Nov 08, 2017 (151)
5 GNOMAD ss2747196401 Nov 08, 2017 (151)
6 GNOMAD ss2804867699 Nov 08, 2017 (151)
7 ILLUMINA ss3022338842 Nov 08, 2017 (151)
8 ILLUMINA ss3652821386 Oct 12, 2018 (152)
9 ILLUMINA ss3726103447 Jul 13, 2019 (153)
10 PAGE_CC ss3771100647 Jul 13, 2019 (153)
11 EVA ss3823997995 Apr 25, 2020 (154)
12 TOPMED ss4600703625 Apr 26, 2021 (155)
13 ExAC NC_000004.11 - 3534135 Oct 12, 2018 (152)
14 gnomAD - Genomes NC_000004.12 - 3532408 Apr 26, 2021 (155)
15 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3475567 (NC_000004.11:3534134:G:G 174015/174026, NC_000004.11:3534134:G:A 11/174026)
Row 3475568 (NC_000004.11:3534134:G:G 174025/174026, NC_000004.11:3534134:G:C 1/174026)

- Jul 13, 2019 (153)
16 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3475567 (NC_000004.11:3534134:G:G 174015/174026, NC_000004.11:3534134:G:A 11/174026)
Row 3475568 (NC_000004.11:3534134:G:G 174025/174026, NC_000004.11:3534134:G:C 1/174026)

- Jul 13, 2019 (153)
17 GO Exome Sequencing Project NC_000004.11 - 3534135 Oct 12, 2018 (152)
18 The PAGE Study NC_000004.12 - 3532408 Jul 13, 2019 (153)
19 TopMed NC_000004.12 - 3532408 Apr 26, 2021 (155)
20 ALFA NC_000004.12 - 3532408 Apr 26, 2021 (155)
Help

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
7365531, 456241, ss712580558, ss1687408114, ss1958652411, ss2734374759, ss2747196401, ss2804867699, ss3022338842, ss3652821386, ss3823997995 NC_000004.11:3534134:G:A NC_000004.12:3532407:G:A (self)
138369805, 322116, 438081181, 53335784, ss3726103447, ss3771100647, ss4600703625 NC_000004.12:3532407:G:A NC_000004.12:3532407:G:A (self)
ss2734374759 NC_000004.11:3534134:G:C NC_000004.12:3532407:G:C (self)
Help

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

No publications for rs375417190

Help

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.

Software version is: 2.0.1.post761+d5e8e07