rs143216483
Variant names:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_001636.4(SLC25A6):c.429G>A(p.Ala143Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0034 in 1,613,714 control chromosomes in the GnomAD database, including 14 homozygotes. There are 2,624 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 0.0023 ( 0 hom., 171 hem., cov: 32)
Exomes 𝑓: 0.0035 ( 14 hom. 2453 hem. )
Consequence
SLC25A6
NM_001636.4 synonymous
NM_001636.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.191
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.46).
BP6
Variant X-1389410-C-T is Benign according to our data. Variant chrX-1389410-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 788322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.191 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 171 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A6 | ENST00000381401.11 | c.429G>A | p.Ala143Ala | synonymous_variant | Exon 2 of 4 | 1 | NM_001636.4 | ENSP00000370808.5 | ||
SLC25A6 | ENST00000475167.6 | n.622G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
SLC25A6 | ENST00000484026.6 | n.610G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 351AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.00230 AC XY: 171AN XY: 74340
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GnomAD3 exomes AF: 0.00190 AC: 476AN: 251174Hom.: 2 AF XY: 0.00194 AC XY: 263AN XY: 135754
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GnomAD4 exome AF: 0.00352 AC: 5137AN: 1461396Hom.: 14 Cov.: 33 AF XY: 0.00337 AC XY: 2453AN XY: 726984
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GnomAD4 genome AF: 0.00230 AC: 351AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.00230 AC XY: 171AN XY: 74468
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at