rs141213807
Variant summary
Our verdict is Benign. The variant received -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_138773.4(SLC25A46):c.767A>G(p.Lys256Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00241 in 1,613,730 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_138773.4 missense
Scores
Clinical Significance
Conservation
Publications
- neuropathy, hereditary motor and sensory, type 6BInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), ClinGen
- pontocerebellar hypoplasia, type 1EInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- hereditary motor and sensory neuropathy type 6Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- pontocerebellar hypoplasia type 1Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Leigh syndromeInheritance: AR Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -18 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_138773.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC25A46 | NM_138773.4 | MANE Select | c.767A>G | p.Lys256Arg | missense | Exon 8 of 8 | NP_620128.1 | ||
| SLC25A46 | NM_001303250.3 | c.494A>G | p.Lys165Arg | missense | Exon 8 of 8 | NP_001290179.1 | |||
| SLC25A46 | NR_138151.2 | n.1006A>G | non_coding_transcript_exon | Exon 9 of 9 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SLC25A46 | ENST00000355943.8 | TSL:1 MANE Select | c.767A>G | p.Lys256Arg | missense | Exon 8 of 8 | ENSP00000348211.3 | ||
| SLC25A46 | ENST00000504098.1 | TSL:5 | c.329A>G | p.Lys110Arg | missense | Exon 7 of 7 | ENSP00000425708.1 | ||
| SLC25A46 | ENST00000513807.5 | TSL:2 | c.281A>G | p.Lys94Arg | missense | Exon 8 of 8 | ENSP00000421134.1 |
Frequencies
GnomAD3 genomes AF: 0.00187 AC: 284AN: 152042Hom.: 2 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00216 AC: 543AN: 250884 AF XY: 0.00234 show subpopulations
GnomAD4 exome AF: 0.00247 AC: 3609AN: 1461570Hom.: 13 Cov.: 32 AF XY: 0.00245 AC XY: 1778AN XY: 727100 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00187 AC: 284AN: 152160Hom.: 2 Cov.: 32 AF XY: 0.00198 AC XY: 147AN XY: 74384 show subpopulations
Age Distribution
ClinVar
ClinVar submissions as Germline
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at