rs1999263

Positions:

• chr9-112447393-C-A
• chr9-112447393-C-G

Variant summary

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

The NM_032303.5(HSDL2):​c.865+5623C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 151,874 control chromosomes in the GnomAD database, including 21,456 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 0.53 (21456 hom., cov: 31)
• Consequence: HSDL2 NM_032303.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

Genes affected

HSDL2 (HGNC:18572): (hydroxysteroid dehydrogenase like 2) Predicted to enable oxidoreductase activity. Located in mitochondrion and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

HSDL2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSDL2	NM_032303.5	c.865+5623C>A		intron_variant		ENST00000398805.8	NP_115679.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSDL2	ENST00000398805.8	c.865+5623C>A		intron_variant		1	NM_032303.5	ENSP00000381785.3

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80594 AN: 151756 Hom.: 21448 Cov.: 31

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.497

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.531 AC: 80634 AN: 151874 Hom.: 21456 Cov.: 31 AF XY: 0.528 AC XY: 39215 AN XY: 74212

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.596

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.543

Gnomad4 OTH AF: 0.495

Alfa AF: 0.478 Hom.: 2898

Bravo AF: 0.523

Asia WGS AF: 0.528 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1999263; hg19: chr9-115209673;