rs1143655
Variant names:
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_001636.4(SLC25A6):c.267C>T(p.Phe89Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00278 in 1,614,166 control chromosomes in the GnomAD database, including 131 homozygotes. There are 1,949 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.015 ( 78 hom., 1030 hem., cov: 32)
Exomes 𝑓: 0.0015 ( 53 hom. 919 hem. )
Consequence
SLC25A6
NM_001636.4 synonymous
NM_001636.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.393
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 -19 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant X-1389572-G-A is Benign according to our data. Variant chrX-1389572-G-A is described in ClinVar as [Benign]. Clinvar id is 785691.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.393 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A6 | ENST00000381401.11 | c.267C>T | p.Phe89Phe | synonymous_variant | Exon 2 of 4 | 1 | NM_001636.4 | ENSP00000370808.5 | ||
SLC25A6 | ENST00000475167.6 | n.460C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
SLC25A6 | ENST00000484026.6 | n.448C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0148 AC: 2252AN: 152170Hom.: 77 Cov.: 32 AF XY: 0.0138 AC XY: 1024AN XY: 74348
GnomAD3 genomes
AF:
AC:
2252
AN:
152170
Hom.:
Cov.:
32
AF XY:
AC XY:
1024
AN XY:
74348
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00377 AC: 949AN: 251492Hom.: 29 AF XY: 0.00260 AC XY: 353AN XY: 135922
GnomAD3 exomes
AF:
AC:
949
AN:
251492
Hom.:
AF XY:
AC XY:
353
AN XY:
135922
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00152 AC: 2222AN: 1461878Hom.: 53 Cov.: 38 AF XY: 0.00126 AC XY: 919AN XY: 727238
GnomAD4 exome
AF:
AC:
2222
AN:
1461878
Hom.:
Cov.:
38
AF XY:
AC XY:
919
AN XY:
727238
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0149 AC: 2263AN: 152288Hom.: 78 Cov.: 32 AF XY: 0.0138 AC XY: 1030AN XY: 74476
GnomAD4 genome
AF:
AC:
2263
AN:
152288
Hom.:
Cov.:
32
AF XY:
AC XY:
1030
AN XY:
74476
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at