rs757342761
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_138773.4(SLC25A46):c.804G>A(p.Thr268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,550 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000035 ( 0 hom. )
Consequence
SLC25A46
NM_138773.4 synonymous
NM_138773.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.307
Genes affected
SLC25A46 (HGNC:25198): (solute carrier family 25 member 46) This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 5-110761329-G-A is Benign according to our data. Variant chr5-110761329-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 475802.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A46 | NM_138773.4 | c.804G>A | p.Thr268= | synonymous_variant | 8/8 | ENST00000355943.8 | |
SLC25A46 | NM_001303250.3 | c.531G>A | p.Thr177= | synonymous_variant | 8/8 | ||
SLC25A46 | NM_001303249.3 | c.679-118G>A | intron_variant | ||||
SLC25A46 | NR_138151.2 | n.1043G>A | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000355943.8 | c.804G>A | p.Thr268= | synonymous_variant | 8/8 | 1 | NM_138773.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 151972Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000399 AC: 10AN: 250884Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135582
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GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461578Hom.: 0 Cov.: 32 AF XY: 0.0000426 AC XY: 31AN XY: 727096
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 151972Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74222
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Neuropathy, hereditary motor and sensory, type 6B Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at