Variant X-119469705-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001152.5(SLC25A5):c.156A>G(p.Lys52=) variant causes a synonymous 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 Likely benign (★).

Frequency

Genomes: 𝑓 0.00072 ( 0 hom., 0 hem., cov: 0)

Exomes 𝑓: 0.00029 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

SLC25A5
NM_001152.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.64

Variant links:

Genes affected

SLC25A5 (HGNC:10991): (solute carrier family 25 member 5) This gene is a member of the mitochondrial carrier subfamily of solute carrier protein genes. The product of this gene functions as a gated pore that translocates ADP from the cytoplasm into the mitochondrial matrix and ATP from the mitochondrial matrix into the cytoplasm. The protein forms a homodimer embedded in the inner mitochondria membrane. Suppressed expression of this gene has been shown to induce apoptosis and inhibit tumor growth. The human genome contains several non-transcribed pseudogenes of this gene.[provided by RefSeq, Jun 2013]

SLC25A5 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant X-119469705-A-G is Benign according to our data. Variant chrX-119469705-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3033285.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.64 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A5	NM_001152.5 linkuse as main transcript	c.156A>G	p.Lys52=	synonymous_variant	2/4	ENST00000317881.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
SLC25A5	ENST00000317881.9 linkuse as main transcript	c.156A>G	p.Lys52=	synonymous_variant	2/4	1	NM_001152.5	P1
SLC25A5	ENST00000460013.1 linkuse as main transcript	n.152A>G		non_coding_transcript_exon_variant	2/4	3
SLC25A5	ENST00000475354.1 linkuse as main transcript	n.70-37A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

20969

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

3333

FAILED QC

Gnomad AFR

AF:

0.00191

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00105

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000347

Gnomad OTH

AF:

0.00362

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000285

AC:

196

AN:

687546

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

147550

show subpopulations

Gnomad4 AFR exome

AF:

0.000944

Gnomad4 AMR exome

AF:

0.00141

Gnomad4 ASJ exome

AF:

0.000578

Gnomad4 EAS exome

AF:

0.000251

Gnomad4 SAS exome

AF:

0.000719

Gnomad4 FIN exome

AF:

0.00123

Gnomad4 NFE exome

AF:

0.000194

Gnomad4 OTH exome

AF:

0.000231

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000715

AC:

AN:

20977

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

3339

show subpopulations

Gnomad4 AFR

AF:

0.00190

Gnomad4 AMR

AF:

0.00104

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000347

Gnomad4 OTH

AF:

0.00355

Alfa

AF:

0.0229

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SLC25A5-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 15, 2019

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over