rs12538145

chr7-96169129-G-C

Variant summary

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

The NM_014251.3(SLC25A13):c.1311+916C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0384 in 152,196 control chromosomes in the GnomAD database, including 164 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 0.038 (164 hom., cov: 32)
• Consequence: SLC25A13 NM_014251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A13	NM_014251.3	c.1311+916C>G		intron_variant		ENST00000265631.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A13	ENST00000265631.10	c.1311+916C>G		intron_variant		1	NM_014251.3	A1
SLC25A13	ENST00000416240.6	c.1314+916C>G		intron_variant		1		P5
SLC25A13	ENST00000490072.5	n.378+916C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5846 AN: 152080 Hom.: 164 Cov.: 32

Gnomad AFR AF: 0.00922

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.0846

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0170

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0430

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0384 AC: 5845 AN: 152196 Hom.: 164 Cov.: 32 AF XY: 0.0407 AC XY: 3026 AN XY: 74410

Gnomad4 AFR AF: 0.00919

Gnomad4 AMR AF: 0.0846

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.0429

Gnomad4 OTH AF: 0.0265

Alfa AF: 0.0454 Hom.: 21

Bravo AF: 0.0379

Asia WGS AF: 0.0110 AC: 39 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.9
Dann	Benign	0.48

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: rs12538145; hg19: chr7-95798441;