chr7-96187919-C-A

Variant names:

• chr7-96187919-C-A
• rs1029391
• NM_014251.3:c.933+1375G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

SLC25A13 Gene-Disease associations (from GenCC):

• citrin deficiency

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• citrullinemia, type II, adult-onset

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia
• neonatal intrahepatic cholestasis due to citrin deficiency

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet
• citrullinemia type II

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014251.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A13	NM_014251.3	MANE Select	c.933+1375G>T		intron	N/A	NP_055066.1	Q9UJS0-1
	SLC25A13	NM_001160210.2		c.933+1375G>T		intron	N/A	NP_001153682.1	Q9UJS0-2
	SLC25A13	NR_027662.2		n.959+1375G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A13	ENST00000265631.10	TSL:1 MANE Select	c.933+1375G>T		intron	N/A	ENSP00000265631.6	Q9UJS0-1
	SLC25A13	ENST00000416240.6	TSL:1	c.933+1375G>T		intron	N/A	ENSP00000400101.2	Q9UJS0-2
	SLC25A13	ENST00000856215.1		c.933+1375G>T		intron	N/A	ENSP00000526274.1

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

African (AFR) AF: 0.507 AC: 21014 AN: 41448

American (AMR) AF: 0.615 AC: 9401 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2562 AN: 3472

East Asian (EAS) AF: 0.388 AC: 1996 AN: 5150

South Asian (SAS) AF: 0.438 AC: 2105 AN: 4810

European-Finnish (FIN) AF: 0.632 AC: 6668 AN: 10558

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42571 AN: 67958

Other (OTH) AF: 0.584 AC: 1232 AN: 2108

Alfa AF: 0.610 Hom.: 38126

Bravo AF: 0.585

Asia WGS AF: 0.397 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	18
DANN	Benign	0.59
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1029391; hg19: chr7-95817231;