Variant 17-81715021-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_012140.5(SLC25A10):c.162C>T(p.Thr54Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0911 in 1,609,912 control chromosomes in the GnomAD database, including 7,442 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 0.072 ( 535 hom., cov: 33)

Exomes 𝑓: 0.093 ( 6907 hom. )

Consequence

SLC25A10
NM_012140.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.73

Variant links:

Genes affected

SLC25A10 (HGNC:10980): (solute carrier family 25 member 10) This gene encodes a member of a family of proteins that translocate small metabolites across the mitochondrial membrane. The encoded protein exchanges dicarboxylates, such as malate and succinate, for phosphate, sulfate, and other small molecules, thereby providing substrates for metabolic processes including the Krebs cycle and fatty acid synthesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Aug 2012]

SLC25A10 links:

ENSG00000262660 (HGNC:):

ENSG00000262660 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP7

Synonymous conserved (PhyloP=-3.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.099 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A10	NM_012140.5 link	c.162C>T	p.Thr54Thr	synonymous_variant	2/11	ENST00000350690.10	NP_036272.2	Q9UBX3-1A0A0S2Z382

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A10	ENST00000350690.10 link	c.162C>T	p.Thr54Thr	synonymous_variant	2/11	1	NM_012140.5	ENSP00000345580.5		Q9UBX3-1
ENSG00000262660	ENST00000571730.1 link	c.627C>T	p.Thr209Thr	synonymous_variant	6/15	2		ENSP00000461324.1		B4DLN1

Frequencies

GnomAD3 genomes

AF:

0.0722

AC:

10986

AN:

152218

Hom.:

534

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0215

Gnomad AMI

AF:

0.0703

Gnomad AMR

AF:

0.0703

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0380

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.0942

GnomAD3 exomes

AF:

0.0753

AC:

18398

AN:

244380

Hom.:

889

AF XY:

0.0766

AC XY:

10224

AN XY:

133406

show subpopulations

Gnomad AFR exome

AF:

0.0170

Gnomad AMR exome

AF:

0.0470

Gnomad ASJ exome

AF:

0.109

Gnomad EAS exome

AF:

0.000164

Gnomad SAS exome

AF:

0.0394

Gnomad FIN exome

AF:

0.127

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.0923

GnomAD4 exome

AF:

0.0931

AC:

135681

AN:

1457576

Hom.:

6907

Cov.:

AF XY:

0.0916

AC XY:

66408

AN XY:

725248

show subpopulations

Gnomad4 AFR exome

AF:

0.0158

Gnomad4 AMR exome

AF:

0.0505

Gnomad4 ASJ exome

AF:

0.116

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0392

Gnomad4 FIN exome

AF:

0.126

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.0893

GnomAD4 genome

AF:

0.0721

AC:

10982

AN:

152336

Hom.:

535

Cov.:

AF XY:

0.0712

AC XY:

5304

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.0214

Gnomad4 AMR

AF:

0.0702

Gnomad4 ASJ

AF:

0.117

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0381

Gnomad4 FIN

AF:

0.118

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.0937

Alfa

AF:

0.0876

Hom.:

400

Bravo

AF:

0.0667

Asia WGS

AF:

0.0150

AC:

AN:

3478

EpiCase

AF:

0.102

EpiControl

AF:

0.106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

2.1

DANN

Benign

0.68

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over