17-42552971-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_000413.4(HSD17B1):c.38C>T(p.Ser13Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000041 in 1,461,790 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 (★).
Frequency
Consequence
NM_000413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B1 | NM_000413.4 | c.38C>T | p.Ser13Leu | missense_variant | Exon 1 of 6 | ENST00000585807.6 | NP_000404.2 | |
HSD17B1 | NM_001330219.3 | c.38C>T | p.Ser13Leu | missense_variant | Exon 1 of 6 | NP_001317148.1 | ||
HSD17B1 | NR_144397.2 | n.49C>T | non_coding_transcript_exon_variant | Exon 1 of 5 | ||||
HSD17B1-AS1 | NR_144402.1 | n.1832G>A | non_coding_transcript_exon_variant | Exon 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251192Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135816
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461790Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 727196
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.38C>T (p.S13L) 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 38, causing the serine (S) at amino acid position 13 to be replaced by a leucine (L). 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