rs6644950

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001636.4(SLC25A6):​c.687C>T​(p.Tyr229Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0141 in 1,613,348 control chromosomes in the GnomAD database, including 481 homozygotes. There are 11,322 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 0.012 ( 44 hom., 929 hem., cov: 33)
Exomes 𝑓: 0.014 ( 437 hom. 10393 hem. )

Consequence

SLC25A6
NM_001636.4 synonymous

Scores

1
1

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.54
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant X-1387331-G-A is Benign according to our data. Variant chrX-1387331-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3032859.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=2.54 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC25A6NM_001636.4 linkc.687C>T p.Tyr229Tyr synonymous_variant Exon 3 of 4 ENST00000381401.11 NP_001627.2 P12236Q6I9V5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC25A6ENST00000381401.11 linkc.687C>T p.Tyr229Tyr synonymous_variant Exon 3 of 4 1 NM_001636.4 ENSP00000370808.5 P12236
SLC25A6ENST00000475167.6 linkn.880C>T non_coding_transcript_exon_variant Exon 4 of 4 2
SLC25A6ENST00000484026.6 linkn.*14C>T downstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.0122
AC:
1850
AN:
152194
Hom.:
44
Cov.:
33
AF XY:
0.0125
AC XY:
929
AN XY:
74340
show subpopulations
Gnomad AFR
AF:
0.00183
Gnomad AMI
AF:
0.0274
Gnomad AMR
AF:
0.00380
Gnomad ASJ
AF:
0.0170
Gnomad EAS
AF:
0.122
Gnomad SAS
AF:
0.0149
Gnomad FIN
AF:
0.0130
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0113
Gnomad OTH
AF:
0.00955
GnomAD3 exomes
AF:
0.0193
AC:
4843
AN:
250462
Hom.:
173
AF XY:
0.0196
AC XY:
2657
AN XY:
135502
show subpopulations
Gnomad AFR exome
AF:
0.00154
Gnomad AMR exome
AF:
0.00333
Gnomad ASJ exome
AF:
0.0159
Gnomad EAS exome
AF:
0.128
Gnomad SAS exome
AF:
0.0163
Gnomad FIN exome
AF:
0.0170
Gnomad NFE exome
AF:
0.0110
Gnomad OTH exome
AF:
0.0136
GnomAD4 exome
AF:
0.0143
AC:
20841
AN:
1461036
Hom.:
437
Cov.:
41
AF XY:
0.0143
AC XY:
10393
AN XY:
726850
show subpopulations
Gnomad4 AFR exome
AF:
0.00155
Gnomad4 AMR exome
AF:
0.00315
Gnomad4 ASJ exome
AF:
0.0182
Gnomad4 EAS exome
AF:
0.116
Gnomad4 SAS exome
AF:
0.0156
Gnomad4 FIN exome
AF:
0.0163
Gnomad4 NFE exome
AF:
0.0112
Gnomad4 OTH exome
AF:
0.0140
GnomAD4 genome
AF:
0.0122
AC:
1852
AN:
152312
Hom.:
44
Cov.:
33
AF XY:
0.0125
AC XY:
929
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00183
Gnomad4 AMR
AF:
0.00379
Gnomad4 ASJ
AF:
0.0170
Gnomad4 EAS
AF:
0.122
Gnomad4 SAS
AF:
0.0152
Gnomad4 FIN
AF:
0.0130
Gnomad4 NFE
AF:
0.0113
Gnomad4 OTH
AF:
0.0113
Bravo
AF:
0.0119
EpiCase
AF:
0.00911
EpiControl
AF:
0.0108

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
-0.60
CADD
Benign
1.4
DANN
Uncertain
0.98
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.

Other links and lift over

dbSNP: rs6644950; hg19: chrX-1506224; COSMIC: COSV58431117; COSMIC: COSV58431117; API