1-186189762-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_031935.3(HMCN1):c.16792C>T(p.Arg5598*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000821 in 1,461,432 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Synonymous variant affecting the same amino acid position (i.e. R5598R) has been classified as Likely benign.
Frequency
Consequence
NM_031935.3 stop_gained
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 |
---|---|---|---|---|---|---|---|---|
HMCN1 | NM_031935.3 | c.16792C>T | p.Arg5598* | stop_gained | Exon 107 of 107 | ENST00000271588.9 | NP_114141.2 | |
HMCN1 | XM_011510038.4 | c.16441C>T | p.Arg5481* | stop_gained | Exon 106 of 106 | XP_011508340.1 | ||
HMCN1 | XM_017002437.2 | c.14815C>T | p.Arg4939* | stop_gained | Exon 96 of 96 | XP_016857926.1 | ||
HMCN1 | XM_047431608.1 | c.12616C>T | p.Arg4206* | stop_gained | Exon 84 of 84 | XP_047287564.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152124Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250408Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135314
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461432Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727010
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74440
ClinVar
Submissions by phenotype
Prostate cancer Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at