rs1999263

Variant names:

• chr9-112447393-C-A
• rs1999263
• NM_032303.5:c.865+5623C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

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:31438): (HSDL2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032303.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSDL2	NM_032303.5	MANE Select	c.865+5623C>A		intron	N/A	NP_115679.2
	HSDL2	NM_001195822.2		c.646+5623C>A		intron	N/A	NP_001182751.1
	HSDL2	NR_036651.2		n.757+5623C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSDL2	ENST00000398805.8	TSL:1 MANE Select	c.865+5623C>A		intron	N/A	ENSP00000381785.3
	HSDL2	ENST00000398803.1	TSL:1	c.646+5623C>A		intron	N/A	ENSP00000381783.1
	HSDL2-AS1	ENST00000412934.2	TSL:3	n.287-13280G>T		intron	N/A

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

African (AFR) AF: 0.545 AC: 22582 AN: 41400

American (AMR) AF: 0.491 AC: 7483 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3468

East Asian (EAS) AF: 0.447 AC: 2305 AN: 5160

South Asian (SAS) AF: 0.596 AC: 2870 AN: 4816

European-Finnish (FIN) AF: 0.501 AC: 5277 AN: 10532

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36865 AN: 67936

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.507 Hom.: 6074

Bravo AF: 0.523

Asia WGS AF: 0.528 AC: 1834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.87
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1999263; hg19: chr9-115209673;