15-40458807-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_014952.5(BAHD1):c.343C>T(p.Arg115Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,612,814 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014952.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BAHD1 | NM_014952.5 | c.343C>T | p.Arg115Cys | missense_variant | Exon 2 of 7 | ENST00000416165.6 | NP_055767.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BAHD1 | ENST00000416165.6 | c.343C>T | p.Arg115Cys | missense_variant | Exon 2 of 7 | 1 | NM_014952.5 | ENSP00000396976.1 | ||
BAHD1 | ENST00000561234.5 | c.343C>T | p.Arg115Cys | missense_variant | Exon 2 of 7 | 1 | ENSP00000454150.1 | |||
BAHD1 | ENST00000560846.1 | c.343C>T | p.Arg115Cys | missense_variant | Exon 1 of 6 | 1 | ENSP00000454101.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000406 AC: 1AN: 246278Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134292
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1460600Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726624
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.343C>T (p.R115C) alteration is located in exon 2 (coding exon 1) of the BAHD1 gene. This alteration results from a C to T substitution at nucleotide position 343, causing the arginine (R) at amino acid position 115 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at