1-119445799-C-T

Variant names:

• chr1-119445799-C-T
• rs11805965
• ENST00000457615.1:n.831C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ENSG00000293080 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HSD3BP2		n.119445799C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSD3BP2	ENST00000457615.1	n.831C>T		non_coding_transcript_exon_variant	Exon 3 of 3	6
ENSG00000293080	ENST00000632456.2	n.769-10652G>A		intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756944.1	n.340-10652G>A		intron_variant	Intron 3 of 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

African (AFR) AF: 0.278 AC: 6326 AN: 22792

American (AMR) AF: 0.130 AC: 5430 AN: 41788

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 3278 AN: 21520

East Asian (EAS) AF: 0.0703 AC: 2607 AN: 37068

South Asian (SAS) AF: 0.107 AC: 7741 AN: 72054

European-Finnish (FIN) AF: 0.0343 AC: 1766 AN: 51434

Middle Eastern (MID) AF: 0.172 AC: 792 AN: 4608

European-Non Finnish (NFE) AF: 0.0810 AC: 48804 AN: 602834

Other (OTH) AF: 0.102 AC: 4208 AN: 41358

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

African (AFR) AF: 0.278 AC: 11549 AN: 41480

American (AMR) AF: 0.148 AC: 2266 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 574 AN: 3470

East Asian (EAS) AF: 0.0676 AC: 350 AN: 5180

South Asian (SAS) AF: 0.115 AC: 553 AN: 4822

European-Finnish (FIN) AF: 0.0322 AC: 342 AN: 10608

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.0791 AC: 5382 AN: 68010

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.0847 Hom.: 338

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
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs11805965; hg19: chr1-119988422;