chr7-96120506-GCTACAT-G

Position:

• chr7-96120506-GCTACAT-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_014251.3(SLC25A13):​c.*679_*684del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00757 in 454,400 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0071 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0078 (12 hom.)
• Consequence: SLC25A13 NM_014251.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.170

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 Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 7-96120506-GCTACAT-G is Benign according to our data. Variant chr7-96120506-GCTACAT-G is described in ClinVar as [Likely_benign]. Clinvar id is 1707378.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A13	NM_014251.3	c.*679_*684del		3_prime_UTR_variant	18/18	ENST00000265631.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A13	ENST00000265631.10	c.*679_*684del		3_prime_UTR_variant	18/18	1	NM_014251.3	A1
SLC25A13	ENST00000416240.6	c.*679_*684del		3_prime_UTR_variant	18/18	1		P5

Frequencies

GnomAD3 genomes AF: 0.00708 AC: 1076 AN: 152064 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.00176

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00537

Gnomad ASJ AF: 0.00433

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0110

Gnomad OTH AF: 0.00478

GnomAD3 exomes AF: 0.00640 AC: 870 AN: 136008 Hom.: 2 AF XY: 0.00675 AC XY: 498 AN XY: 73826

Gnomad AFR exome AF: 0.00202

Gnomad AMR exome AF: 0.00196

Gnomad ASJ exome AF: 0.00580

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00213

Gnomad FIN exome AF: 0.0126

Gnomad NFE exome AF: 0.0112

Gnomad OTH exome AF: 0.00896

GnomAD4 exome AF: 0.00782 AC: 2363 AN: 302218 Hom.: 12 AF XY: 0.00729 AC XY: 1255 AN XY: 172250

Gnomad4 AFR exome AF: 0.00269

Gnomad4 AMR exome AF: 0.00194

Gnomad4 ASJ exome AF: 0.00538

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00205

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.0113

Gnomad4 OTH exome AF: 0.00847

GnomAD4 genome AF: 0.00707 AC: 1076 AN: 152182 Hom.: 2 Cov.: 32 AF XY: 0.00726 AC XY: 540 AN XY: 74400

Gnomad4 AFR AF: 0.00176

Gnomad4 AMR AF: 0.00537

Gnomad4 ASJ AF: 0.00433

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0110

Gnomad4 OTH AF: 0.00473

Alfa AF: 0.00829 Hom.: 1

Bravo AF: 0.00613

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 16, 2021

See Variant Classification Assertion Criteria. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs532132551; hg19: chr7-95749818;