chr3-121632142-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005335.6(HCLS1):c.1283C>T(p.Ala428Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,418 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005335.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HCLS1 | NM_005335.6 | c.1283C>T | p.Ala428Val | missense_variant | 13/14 | ENST00000314583.8 | |
HCLS1 | NM_001292041.2 | c.1172C>T | p.Ala391Val | missense_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HCLS1 | ENST00000314583.8 | c.1283C>T | p.Ala428Val | missense_variant | 13/14 | 1 | NM_005335.6 | P1 | |
HCLS1 | ENST00000428394.6 | c.1172C>T | p.Ala391Val | missense_variant | 12/13 | 2 | |||
HCLS1 | ENST00000473883.5 | n.2086C>T | non_coding_transcript_exon_variant | 8/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000484 AC: 12AN: 248162Hom.: 0 AF XY: 0.0000298 AC XY: 4AN XY: 134398
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461286Hom.: 0 Cov.: 36 AF XY: 0.00000413 AC XY: 3AN XY: 726926
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at