17-42552940-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000413.4(HSD17B1):c.7C>T(p.Arg3Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.7C>T | p.Arg3Cys | missense_variant | 1/6 | ENST00000585807.6 | |
HSD17B1-AS1 | NR_144402.1 | n.1863G>A | non_coding_transcript_exon_variant | 1/1 | |||
HSD17B1 | NM_001330219.3 | c.7C>T | p.Arg3Cys | missense_variant | 1/6 | ||
HSD17B1 | NR_144397.2 | n.18C>T | non_coding_transcript_exon_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B1 | ENST00000585807.6 | c.7C>T | p.Arg3Cys | missense_variant | 1/6 | 1 | NM_000413.4 | P4 | |
HSD17B1-AS1 | ENST00000590513.3 | n.1902G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251052Hom.: 0 AF XY: 0.000191 AC XY: 26AN XY: 135812
GnomAD4 exome AF: 0.0000725 AC: 106AN: 1461606Hom.: 0 Cov.: 30 AF XY: 0.0000633 AC XY: 46AN XY: 727100
GnomAD4 genome ? AF: 0.0000984 AC: 15AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000805 AC XY: 6AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.7C>T (p.R3C) alteration is located in exon 1 (coding exon 1) of the HSD17B1 gene. This alteration results from a C to T substitution at nucleotide position 7, causing the arginine (R) at amino acid position 3 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