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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.

rs143912947

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr13:23869319 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/264690, TOPMED)
A=0.000008 (2/247750, GnomAD_exome)
A=0.000021 (3/140250, GnomAD) (+ 3 more)
A=0.000008 (1/120586, ExAC)
A=0.00007 (1/14050, ALFA)
A=0.00008 (1/13006, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MIPEP : Missense Variant
Publications
1 citation
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 14050 G=0.99993 A=0.00007
European Sub 9690 G=0.9999 A=0.0001
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 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 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=0.000


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=0.999992 A=0.000008
gnomAD - Exomes Global Study-wide 247750 G=0.999992 A=0.000008
gnomAD - Exomes European Sub 134336 G=0.999985 A=0.000015
gnomAD - Exomes Asian Sub 47898 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 33342 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16182 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9956 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 6036 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140250 G=0.999979 A=0.000021
gnomAD - Genomes European Sub 75946 G=0.99996 A=0.00004
gnomAD - Genomes African Sub 42040 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13658 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 120586 G=0.999992 A=0.000008
ExAC Europe Sub 73124 G=0.99999 A=0.00001
ExAC Asian Sub 24580 G=1.00000 A=0.00000
ExAC American Sub 11574 G=1.00000 A=0.00000
ExAC African Sub 10406 G=1.00000 A=0.00000
ExAC Other Sub 902 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 14050 G=0.99993 A=0.00007
Allele Frequency Aggregator European Sub 9690 G=0.9999 A=0.0001
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.99992 A=0.00008
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
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 13 NC_000013.11:g.23869319G>A
GRCh37.p13 chr 13 NC_000013.10:g.24443458G>A
MIPEP RefSeqGene NG_052977.1:g.25130C>T
Gene: MIPEP, mitochondrial intermediate peptidase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MIPEP transcript NM_005932.4:c.916C>T L [CTC] > F [TTC] Coding Sequence Variant
mitochondrial intermediate peptidase NP_005923.3:p.Leu306Phe L (Leu) > F (Phe) Missense Variant
MIPEP transcript variant X1 XM_011535097.3:c.730C>T L [CTC] > F [TTC] Coding Sequence Variant
mitochondrial intermediate peptidase isoform X1 XP_011533399.1:p.Leu244Phe L (Leu) > F (Phe) Missense Variant
MIPEP transcript variant X2 XM_011535098.4:c.916C>T L [CTC] > F [TTC] Coding Sequence Variant
mitochondrial intermediate peptidase isoform X2 XP_011533400.1:p.Leu306Phe L (Leu) > F (Phe) Missense Variant
MIPEP transcript variant X3 XM_047430368.1:c.730C>T L [CTC] > F [TTC] Coding Sequence Variant
mitochondrial intermediate peptidase isoform X3 XP_047286324.1:p.Leu244Phe L (Leu) > F (Phe) Missense 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.

Allele: A (allele ID: 205201 )
ClinVar Accession Disease Names Clinical Significance
RCV000412517.2 Lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndrome Pathogenic
RCV000602489.2 Cardiomyopathy,Infantile muscular hypotonia,Left ventricular noncompaction Uncertain-Significance
RCV001042479.3 not provided Uncertain-Significance
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
GRCh38.p14 chr 13 NC_000013.11:g.23869319= NC_000013.11:g.23869319G>A
GRCh37.p13 chr 13 NC_000013.10:g.24443458= NC_000013.10:g.24443458G>A
MIPEP RefSeqGene NG_052977.1:g.25130= NG_052977.1:g.25130C>T
MIPEP transcript NM_005932.4:c.916= NM_005932.4:c.916C>T
MIPEP transcript NM_005932.3:c.916= NM_005932.3:c.916C>T
MIPEP transcript variant X2 XM_011535098.4:c.916= XM_011535098.4:c.916C>T
MIPEP transcript variant X2 XM_011535098.3:c.916= XM_011535098.3:c.916C>T
MIPEP transcript variant X2 XM_011535098.2:c.916= XM_011535098.2:c.916C>T
MIPEP transcript variant X2 XM_011535098.1:c.916= XM_011535098.1:c.916C>T
MIPEP transcript variant X1 XM_011535097.3:c.730= XM_011535097.3:c.730C>T
MIPEP transcript variant X1 XM_011535097.2:c.730= XM_011535097.2:c.730C>T
MIPEP transcript variant X1 XM_011535097.1:c.730= XM_011535097.1:c.730C>T
MIPEP transcript variant X3 XM_047430368.1:c.730= XM_047430368.1:c.730C>T
mitochondrial intermediate peptidase NP_005923.3:p.Leu306= NP_005923.3:p.Leu306Phe
mitochondrial intermediate peptidase isoform X2 XP_011533400.1:p.Leu306= XP_011533400.1:p.Leu306Phe
mitochondrial intermediate peptidase isoform X1 XP_011533399.1:p.Leu244= XP_011533399.1:p.Leu244Phe
mitochondrial intermediate peptidase isoform X3 XP_047286324.1:p.Leu244= XP_047286324.1:p.Leu244Phe
mitochondrial intermediate peptidase NP_005923.2:p.Leu306= NP_005923.2:p.Leu306Phe
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#.

7 SubSNP, 6 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342373015 May 09, 2011 (134)
2 EVA_EXAC ss1691225228 Apr 01, 2015 (144)
3 GNOMAD ss2740313941 Nov 08, 2017 (151)
4 GNOMAD ss2749017440 Nov 08, 2017 (151)
5 GNOMAD ss2917548224 Nov 08, 2017 (151)
6 EVA ss3824796078 Apr 27, 2020 (154)
7 TOPMED ss4939801880 Apr 26, 2021 (155)
8 ExAC NC_000013.10 - 24443458 Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000013.11 - 23869319 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000013.10 - 24443458 Jul 13, 2019 (153)
11 GO Exome Sequencing Project NC_000013.10 - 24443458 Oct 12, 2018 (152)
12 TopMed NC_000013.11 - 23869319 Apr 26, 2021 (155)
13 ALFA NC_000013.11 - 23869319 Apr 26, 2021 (155)
14 ClinVar RCV000412517.2 Oct 16, 2022 (156)
15 ClinVar RCV000602489.2 Oct 16, 2022 (156)
16 ClinVar RCV001042479.3 Oct 16, 2022 (156)
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
1548700, 9555359, 1253471, ss342373015, ss1691225228, ss2740313941, ss2749017440, ss2917548224, ss3824796078 NC_000013.10:24443457:G:A NC_000013.11:23869318:G:A (self)
RCV000412517.2, RCV000602489.2, RCV001042479.3, 425386473, 155347538, 5283154999, ss4939801880 NC_000013.11:23869318:G:A NC_000013.11:23869318:G:A (self)
Help

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

1 citation for rs143912947
PMID Title Author Year Journal
27799064 MIPEP recessive variants cause a syndrome of left ventricular non-compaction, hypotonia, and infantile death. Eldomery MK et al. 2016 Genome medicine
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