3-66236234-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_001379210.1(SLC25A26):c.34-310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.95 (52267 hom., cov: 19)
  • Failed GnomAD Quality Control
• Consequence: SLC25A26 NM_001379210.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17

Genes affected

SLC25A26 (HGNC:20661): (solute carrier family 25 member 26) This gene is a member of the mitochondrial carrier family which includes nuclear-encoded transporters localized on the inner mitochondrial membranes. Members of the family transport important small molecules across the mitochondrial inner membrane. This protein is involved in the transport of S-adenosylmethionine (SAM) into the mitochondria. Mutations in this gene are associated with combined oxidative phosphorylation deficiency 28. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 3-66236234-G-A is Benign according to our data. Variant chr3-66236234-G-A is described in ClinVar as [Benign]. Clinvar id is 683877.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd at 52262 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A26	NM_001379210.1	c.34-310G>A		intron_variant		ENST00000354883.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A26	ENST00000354883.11	c.34-310G>A		intron_variant		2	NM_001379210.1	P1

Frequencies

GnomAD3 genomes AF: 0.951 AC: 110128 AN: 115772 Hom.: 52262 Cov.: 19

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.951

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.951 AC: 110138 AN: 115782 Hom.: 52267 Cov.: 19 AF XY: 0.952 AC XY: 51621 AN XY: 54212

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.950

Gnomad4 ASJ AF: 0.952

Gnomad4 EAS AF: 0.955

Gnomad4 SAS AF: 0.969

Gnomad4 FIN AF: 0.947

Gnomad4 NFE AF: 0.949

Gnomad4 OTH AF: 0.951

Alfa AF: 0.999 Hom.: 8031

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.65
Dann	Benign	0.33

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: rs185555999; hg19: chr3-66286658;