NM_001636.4:c.762C>T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001636.4(SLC25A6):​c.762C>T​(p.Thr254Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00322 in 1,610,794 control chromosomes in the GnomAD database, including 10 homozygotes. There are 2,498 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0022 ( 1 hom., 151 hem., cov: 32)
Exomes 𝑓: 0.0033 ( 9 hom. 2347 hem. )

Consequence

SLC25A6
NM_001636.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.404
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant X-1386737-G-A is Benign according to our data. Variant chrX-1386737-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 774972.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.404 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 151 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC25A6NM_001636.4 linkc.762C>T p.Thr254Thr synonymous_variant Exon 4 of 4 ENST00000381401.11 NP_001627.2 P12236Q6I9V5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC25A6ENST00000381401.11 linkc.762C>T p.Thr254Thr synonymous_variant Exon 4 of 4 1 NM_001636.4 ENSP00000370808.5 P12236

Frequencies

GnomAD3 genomes
AF:
0.00220
AC:
335
AN:
152018
Hom.:
1
Cov.:
32
AF XY:
0.00203
AC XY:
151
AN XY:
74238
show subpopulations
Gnomad AFR
AF:
0.000846
Gnomad AMI
AF:
0.00220
Gnomad AMR
AF:
0.00177
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00123
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00372
Gnomad OTH
AF:
0.000958
GnomAD3 exomes
AF:
0.00218
AC:
541
AN:
248074
Hom.:
0
AF XY:
0.00230
AC XY:
308
AN XY:
134102
show subpopulations
Gnomad AFR exome
AF:
0.000743
Gnomad AMR exome
AF:
0.00100
Gnomad ASJ exome
AF:
0.000908
Gnomad EAS exome
AF:
0.0000554
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00227
Gnomad NFE exome
AF:
0.00371
Gnomad OTH exome
AF:
0.00333
GnomAD4 exome
AF:
0.00333
AC:
4852
AN:
1458658
Hom.:
9
Cov.:
32
AF XY:
0.00323
AC XY:
2347
AN XY:
725592
show subpopulations
Gnomad4 AFR exome
AF:
0.000540
Gnomad4 AMR exome
AF:
0.000970
Gnomad4 ASJ exome
AF:
0.00131
Gnomad4 EAS exome
AF:
0.0000759
Gnomad4 SAS exome
AF:
0.0000582
Gnomad4 FIN exome
AF:
0.00244
Gnomad4 NFE exome
AF:
0.00402
Gnomad4 OTH exome
AF:
0.00261
GnomAD4 genome
AF:
0.00220
AC:
335
AN:
152136
Hom.:
1
Cov.:
32
AF XY:
0.00203
AC XY:
151
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.000843
Gnomad4 AMR
AF:
0.00177
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00123
Gnomad4 NFE
AF:
0.00372
Gnomad4 OTH
AF:
0.000948
Bravo
AF:
0.00211

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.49
CADD
Benign
0.64
DANN
Benign
0.95

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: rs149117617; hg19: chrX-1505630; API