chr7-96177826-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014251.3(SLC25A13):​c.1178-6302T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,932 control chromosomes in the GnomAD database, including 14,020 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.42 ( 14020 hom., cov: 32)

Consequence

SLC25A13
NM_014251.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.601
Variant links:
Genes affected
SLC25A13 (HGNC:10983): (solute carrier family 25 member 13) This gene is a member of the mitochondrial carrier family. The encoded protein contains four EF-hand Ca(2+) binding motifs in the N-terminal domain, and localizes to mitochondria. The protein catalyzes the exchange of aspartate for glutamate and a proton across the inner mitochondrial membrane, and is stimulated by calcium on the external side of the inner mitochondrial membrane. Mutations in this gene result in citrullinemia, type II. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC25A13NM_014251.3 linkuse as main transcriptc.1178-6302T>C intron_variant ENST00000265631.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC25A13ENST00000265631.10 linkuse as main transcriptc.1178-6302T>C intron_variant 1 NM_014251.3 A1Q9UJS0-1

Frequencies

GnomAD3 genomes
AF:
0.422
AC:
64080
AN:
151814
Hom.:
13979
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.509
Gnomad AMI
AF:
0.144
Gnomad AMR
AF:
0.385
Gnomad ASJ
AF:
0.263
Gnomad EAS
AF:
0.612
Gnomad SAS
AF:
0.561
Gnomad FIN
AF:
0.368
Gnomad MID
AF:
0.439
Gnomad NFE
AF:
0.374
Gnomad OTH
AF:
0.415
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.422
AC:
64181
AN:
151932
Hom.:
14020
Cov.:
32
AF XY:
0.425
AC XY:
31583
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.509
Gnomad4 AMR
AF:
0.386
Gnomad4 ASJ
AF:
0.263
Gnomad4 EAS
AF:
0.612
Gnomad4 SAS
AF:
0.562
Gnomad4 FIN
AF:
0.368
Gnomad4 NFE
AF:
0.374
Gnomad4 OTH
AF:
0.422
Alfa
AF:
0.388
Hom.:
3837
Bravo
AF:
0.421
Asia WGS
AF:
0.605
AC:
2104
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.72
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2375044; hg19: chr7-95807138; API