rs11550233
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001636.4(SLC25A6):c.225T>G(p.Leu75Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000131 in 1,614,122 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 83 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 0.00070 ( 0 hom., 45 hem., cov: 32)
Exomes 𝑓: 0.000072 ( 0 hom. 38 hem. )
Consequence
SLC25A6
NM_001636.4 synonymous
NM_001636.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0300
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 -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant X-1389614-A-C is Benign according to our data. Variant chrX-1389614-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 709133.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-0.03 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 45 gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A6 | ENST00000381401.11 | c.225T>G | p.Leu75Leu | synonymous_variant | Exon 2 of 4 | 1 | NM_001636.4 | ENSP00000370808.5 | ||
SLC25A6 | ENST00000475167.6 | n.418T>G | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 | |||||
SLC25A6 | ENST00000484026.6 | n.406T>G | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000697 AC: 106AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000592 AC XY: 44AN XY: 74308
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GnomAD3 exomes AF: 0.000223 AC: 56AN: 251490Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135920
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GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461882Hom.: 0 Cov.: 38 AF XY: 0.0000523 AC XY: 38AN XY: 727242
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GnomAD4 genome AF: 0.000696 AC: 106AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74436
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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
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
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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