chr17-42554888-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000413.4(HSD17B1):c.937G>T(p.Gly313Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000037 in 1,538,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G313S) has been classified as Likely benign.
Frequency
Consequence
NM_000413.4 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 |
---|---|---|---|---|---|---|---|
HSD17B1 | NM_000413.4 | c.937G>T | p.Gly313Cys | missense_variant | 6/6 | ENST00000585807.6 | |
HSD17B1 | NM_001330219.3 | c.940G>T | p.Gly314Cys | missense_variant | 6/6 | ||
HSD17B1 | NR_144397.2 | n.854G>T | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B1 | ENST00000585807.6 | c.937G>T | p.Gly313Cys | missense_variant | 6/6 | 1 | NM_000413.4 | P4 | |
HSD17B1 | ENST00000225929.5 | c.940G>T | p.Gly314Cys | missense_variant | 6/6 | 2 | A2 | ||
HSD17B1 | ENST00000590299.5 | c.*393G>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 5 | ||||
HSD17B1-AS1 | ENST00000590513.3 | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000139 AC: 2AN: 144020Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80412
GnomAD4 exome AF: 0.0000375 AC: 52AN: 1386848Hom.: 0 Cov.: 56 AF XY: 0.0000365 AC XY: 25AN XY: 685756
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152044Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74258
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at