1-119445799-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457615.1(HSD3BP2):n.831C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0977 in 1,047,638 control chromosomes in the GnomAD database, including 6,596 homozygotes. 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: 𝑓 0.14 (2146 hom., cov: 33)
  • Exomes 𝑓: 0.090 (4450 hom.)
• Consequence: HSD3BP2 ENST00000457615.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

Genes affected

HSD3BP2 (HGNC:5220): (hydroxy-delta-5-steroid dehydrogenase, 3 beta, pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSD3BP2	ENST00000457615.1	n.831C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21354 AN: 152064 Hom.: 2142 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0674

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0791

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.0904 AC: 80952 AN: 895456 Hom.: 4450 Cov.: 13 AF XY: 0.0907 AC XY: 42427 AN XY: 467902

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.130

Gnomad4 ASJ exome AF: 0.152

Gnomad4 EAS exome AF: 0.0703

Gnomad4 SAS exome AF: 0.107

Gnomad4 FIN exome AF: 0.0343

Gnomad4 NFE exome AF: 0.0810

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.141 AC: 21384 AN: 152182 Hom.: 2146 Cov.: 33 AF XY: 0.139 AC XY: 10360 AN XY: 74416

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0676

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0322

Gnomad4 NFE AF: 0.0791

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0824 Hom.: 312

Bravo AF: 0.155

Asia WGS AF: 0.106 AC: 372 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	1.1
Dann	Benign	0.45

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11805965; hg19: chr1-119988422;