rs1704754
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016371.4(HSD17B7):c.-40C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 26)
Exomes 𝑓: 8.6e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HSD17B7
NM_016371.4 5_prime_UTR
NM_016371.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.98
Genes affected
HSD17B7 (HGNC:5215): (hydroxysteroid 17-beta dehydrogenase 7) HSD17B7 encodes an enzyme that functions both as a 17-beta-hydroxysteroid dehydrogenase (EC 1.1.1.62) in the biosynthesis of sex steroids and as a 3-ketosteroid reductase (EC 1.1.1.270) in the biosynthesis of cholesterol (Marijanovic et al., 2003 [PubMed 12829805]).[supplied by OMIM, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B7 | NM_016371.4 | c.-40C>G | 5_prime_UTR_variant | 1/9 | ENST00000254521.8 | NP_057455.1 | ||
HSD17B7 | NM_001304512.2 | c.-40C>G | 5_prime_UTR_variant | 1/4 | NP_001291441.1 | |||
HSD17B7 | NM_001304513.2 | c.-40C>G | 5_prime_UTR_variant | 1/4 | NP_001291442.1 | |||
HSD17B7 | XR_007060779.1 | n.60C>G | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD17B7 | ENST00000254521.8 | c.-40C>G | 5_prime_UTR_variant | 1/9 | 1 | NM_016371.4 | ENSP00000254521 | P1 |
Frequencies
GnomAD3 genomes Cov.: 26
GnomAD3 genomes
Cov.:
26
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.63e-7 AC: 1AN: 1158264Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0AN XY: 586870
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1158264
Hom.:
Cov.:
16
AF XY:
AC XY:
0
AN XY:
586870
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 26
GnomAD4 genome
Cov.:
26
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at