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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457615.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSD3BP2	ENST00000457615.1	TSL:6	n.831C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000293080	ENST00000632456.2	TSL:6	n.769-10652G>A		intron	N/A
	ENSG00000293080	ENST00000756944.1		n.340-10652G>A		intron	N/A

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 v4.9

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;