rs1029391

Positions:

• chr7-96187919-C-A
• chr7-96187919-C-G
• chr7-96187919-C-T

Variant summary

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

The NM_014251.3(SLC25A13):​c.933+1375G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,994 control chromosomes in the GnomAD database, including 26,160 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 0.58 (26160 hom., cov: 32)
• Consequence: SLC25A13 NM_014251.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A13	NM_014251.3	c.933+1375G>T		intron_variant		ENST00000265631.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A13	ENST00000265631.10	c.933+1375G>T		intron_variant		1	NM_014251.3	A1
SLC25A13	ENST00000416240.6	c.933+1375G>T		intron_variant		1		P5
SLC25A13	ENST00000484495.5	n.86+1375G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88464 AN: 151876 Hom.: 26157 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.582 AC: 88489 AN: 151994 Hom.: 26160 Cov.: 32 AF XY: 0.579 AC XY: 42995 AN XY: 74292

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.584

Alfa AF: 0.611 Hom.: 30948

Bravo AF: 0.585

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	18
DANN	Benign	0.59

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: rs1029391; hg19: chr7-95817231;