chr17-42553159-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000413.4(HSD17B1):āc.133C>Gā(p.Arg45Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,613,620 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R45Q) has been classified as Likely benign.
Frequency
Consequence
NM_000413.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD17B1 | NM_000413.4 | c.133C>G | p.Arg45Gly | missense_variant | 2/6 | ENST00000585807.6 | |
HSD17B1-AS1 | NR_144402.1 | n.1644G>C | non_coding_transcript_exon_variant | 1/1 | |||
HSD17B1 | NM_001330219.3 | c.133C>G | p.Arg45Gly | missense_variant | 2/6 | ||
HSD17B1 | NR_144397.2 | n.144C>G | non_coding_transcript_exon_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B1 | ENST00000585807.6 | c.133C>G | p.Arg45Gly | missense_variant | 2/6 | 1 | NM_000413.4 | P4 | |
HSD17B1-AS1 | ENST00000590513.3 | n.1683G>C | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152218Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461402Hom.: 0 Cov.: 36 AF XY: 0.00000825 AC XY: 6AN XY: 727006
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152218Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.133C>G (p.R45G) alteration is located in exon 2 (coding exon 2) of the HSD17B1 gene. This alteration results from a C to G substitution at nucleotide position 133, causing the arginine (R) at amino acid position 45 to be replaced by a glycine (G). 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