chr9-96235464-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000197.2(HSD17B3):c.929G>A(p.Arg310Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,612,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. R310R) has been classified as Likely benign.
Frequency
Consequence
NM_000197.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD17B3 | ENST00000375263.8 | c.929G>A | p.Arg310Lys | missense_variant | Exon 11 of 11 | 1 | NM_000197.2 | ENSP00000364412.3 | ||
ENSG00000285269 | ENST00000643789.1 | n.*2605G>A | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000494818.1 | |||||
ENSG00000285269 | ENST00000643789.1 | n.*2605G>A | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000494818.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249664Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134988
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460170Hom.: 0 Cov.: 29 AF XY: 0.0000138 AC XY: 10AN XY: 726378
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.929G>A (p.R310K) alteration is located in exon 11 (coding exon 11) of the HSD17B3 gene. This alteration results from a G to A substitution at nucleotide position 929, causing the arginine (R) at amino acid position 310 to be replaced by a lysine (K). 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