dbSNP rs7205: SLC25A6:p.Phe136Phe (chrX-1389431-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BA1

The NM_001636.4(SLC25A6):c.408C>T(p.Phe136Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,613,326 control chromosomes in the GnomAD database, including 61,161 homozygotes. There are 216,469 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.31 ( 8165 hom., 22833 hem., cov: 32)

Exomes 𝑓: 0.26 ( 52996 hom. 193636 hem. )

Consequence

SLC25A6
NM_001636.4 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.09

Variant links:

Genes affected

SLC25A6 (HGNC:10992): (solute carrier family 25 member 6) 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 is implicated in the function of the permability transition pore complex (PTPC), which regulates the release of mitochondrial products that induce apoptosis. The human genome contains several non-transcribed pseudogenes of this gene. [provided by RefSeq, Jun 2013]

SLC25A6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant X-1389431-G-A is Benign according to our data. Variant chrX-1389431-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3036125.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=1.09 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A6	NM_001636.4 link	c.408C>T	p.Phe136Phe	synonymous_variant	Exon 2 of 4	ENST00000381401.11	NP_001627.2	P12236Q6I9V5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC25A6	ENST00000381401.11 link	c.408C>T	p.Phe136Phe	synonymous_variant	Exon 2 of 4	1	NM_001636.4	ENSP00000370808.5	P12236
SLC25A6	ENST00000475167.6 link	n.601C>T		non_coding_transcript_exon_variant	Exon 3 of 4	2
SLC25A6	ENST00000484026.6 link	n.589C>T		non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.310

AC:

47061

AN:

151972

Hom.:

8151

Cov.:

AF XY:

0.307

AC XY:

22791

AN XY:

74204

show subpopulations

Gnomad AFR

AF:

0.448

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.298

Gnomad ASJ

AF:

0.300

Gnomad EAS

AF:

0.105

Gnomad SAS

AF:

0.372

Gnomad FIN

AF:

0.227

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.254

Gnomad OTH

AF:

0.302

GnomAD3 exomes

AF:

0.283

AC:

71050

AN:

251204

Hom.:

11092

AF XY:

0.286

AC XY:

38794

AN XY:

135774

show subpopulations

Gnomad AFR exome

AF:

0.459

Gnomad AMR exome

AF:

0.323

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.0888

Gnomad SAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.232

Gnomad NFE exome

AF:

0.255

Gnomad OTH exome

AF:

0.280

GnomAD4 exome

AF:

0.263

AC:

384692

AN:

1461234

Hom.:

52996

Cov.:

AF XY:

0.266

AC XY:

193636

AN XY:

726808

show subpopulations

Gnomad4 AFR exome

AF:

0.454

Gnomad4 AMR exome

AF:

0.324

Gnomad4 ASJ exome

AF:

0.311

Gnomad4 EAS exome

AF:

0.124

Gnomad4 SAS exome

AF:

0.389

Gnomad4 FIN exome

AF:

0.232

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.277

GnomAD4 genome

AF:

0.310

AC:

47099

AN:

152092

Hom.:

8165

Cov.:

AF XY:

0.307

AC XY:

22833

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.448

Gnomad4 AMR

AF:

0.298

Gnomad4 ASJ

AF:

0.300

Gnomad4 EAS

AF:

0.105

Gnomad4 SAS

AF:

0.374

Gnomad4 FIN

AF:

0.227

Gnomad4 NFE

AF:

0.254

Gnomad4 OTH

AF:

0.300

Bravo

AF:

0.320

EpiCase

AF:

0.264

EpiControl

AF:

0.257

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

SLC25A6-related disorder

Benign:1

Feb 16, 2021

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.43

CADD

Benign

7.5

DANN

Benign

0.75

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