rs10252573

Positions:

• chr7-96145811-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014251.3(SLC25A13):​c.1452+745A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,060 control chromosomes in the GnomAD database, including 10,705 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 0.37 (10705 hom., cov: 33)
• Consequence: SLC25A13 NM_014251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A13	NM_014251.3	c.1452+745A>T		intron_variant		ENST00000265631.10	NP_055066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A13	ENST00000265631.10	c.1452+745A>T		intron_variant		1	NM_014251.3	ENSP00000265631.6
SLC25A13	ENST00000416240.6	c.1455+745A>T		intron_variant		1		ENSP00000400101.2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56195 AN: 151942 Hom.: 10690 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.388

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.370 AC: 56244 AN: 152060 Hom.: 10705 Cov.: 33 AF XY: 0.372 AC XY: 27681 AN XY: 74318

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.395

Alfa AF: 0.376 Hom.: 1348

Bravo AF: 0.362

Asia WGS AF: 0.552 AC: 1911 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	12
DANN	Benign	0.88

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

Other links and lift over

dbSNP: rs10252573; hg19: chr7-95775123;