chr16-30985761-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_025193.4(HSD3B7):c.103C>T(p.Arg35Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,452,574 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R35G) has been classified as Likely benign.
Frequency
Consequence
NM_025193.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD3B7 | NM_025193.4 | c.103C>T | p.Arg35Trp | missense_variant | 2/7 | ENST00000297679.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD3B7 | ENST00000297679.10 | c.103C>T | p.Arg35Trp | missense_variant | 2/7 | 1 | NM_025193.4 | P1 | |
ENST00000624286.1 | n.2510G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000218 AC: 5AN: 229224Hom.: 0 AF XY: 0.00000802 AC XY: 1AN XY: 124762
GnomAD4 exome AF: 0.0000186 AC: 27AN: 1452574Hom.: 0 Cov.: 33 AF XY: 0.0000194 AC XY: 14AN XY: 721902
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 20, 2023 | The c.103C>T (p.R35W) alteration is located in exon 2 (coding exon 1) of the HSD3B7 gene. This alteration results from a C to T substitution at nucleotide position 103, causing the arginine (R) at amino acid position 35 to be replaced by a tryptophan (W). 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