17-42554784-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000413.4(HSD17B1):c.833C>G(p.Thr278Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 1,602,756 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 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.833C>G | p.Thr278Ser | missense_variant | 6/6 | ENST00000585807.6 | |
HSD17B1-AS1 | NR_144402.1 | n.19G>C | non_coding_transcript_exon_variant | 1/1 | |||
HSD17B1 | NM_001330219.3 | c.836C>G | p.Thr279Ser | missense_variant | 6/6 | ||
HSD17B1 | NR_144397.2 | n.750C>G | non_coding_transcript_exon_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B1 | ENST00000585807.6 | c.833C>G | p.Thr278Ser | missense_variant | 6/6 | 1 | NM_000413.4 | P4 | |
HSD17B1-AS1 | ENST00000590513.3 | n.58G>C | non_coding_transcript_exon_variant | 1/1 | |||||
HSD17B1 | ENST00000225929.5 | c.836C>G | p.Thr279Ser | missense_variant | 6/6 | 2 | A2 | ||
HSD17B1 | ENST00000590299.5 | c.*289C>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152228Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000173 AC: 4AN: 231776Hom.: 0 AF XY: 0.00000782 AC XY: 1AN XY: 127908
GnomAD4 exome AF: 0.00000620 AC: 9AN: 1450528Hom.: 1 Cov.: 31 AF XY: 0.00000415 AC XY: 3AN XY: 722114
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152228Hom.: 0 Cov.: 34 AF XY: 0.0000672 AC XY: 5AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.833C>G (p.T278S) alteration is located in exon 6 (coding exon 6) of the HSD17B1 gene. This alteration results from a C to G substitution at nucleotide position 833, causing the threonine (T) at amino acid position 278 to be replaced by a serine (S). 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