10-125873806-C-T

Variant names:

• chr10-125873806-C-T
• rs10794030
• NM_018180.3:c.283-6623G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018180.3(DHX32):​c.283-6623G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,002 control chromosomes in the GnomAD database, including 17,011 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 0.47 (17011 hom., cov: 32)
• Consequence: DHX32 NM_018180.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 9 publications found

Genes affected

DHX32 (HGNC:16717): (DEAH-box helicase 32 (putative)) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a member of this family. The function of this member has not been determined. Alternative splicing of this gene generates 2 transcript variants, but the full length nature of one of the variants has not been defined. [provided by RefSeq, Jul 2008]

DHX32 Gene-Disease associations (from GenCC):

• retinal disorder

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
• retinitis pigmentosa

  Inheritance: AR Classification: LIMITED Submitted by: G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DHX32	NM_018180.3	c.283-6623G>A		intron_variant	Intron 1 of 10	ENST00000284690.4	NP_060650.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DHX32	ENST00000284690.4	c.283-6623G>A		intron_variant	Intron 1 of 10	1	NM_018180.3	ENSP00000284690.3
DHX32	ENST00000415732.1	c.283-6623G>A		intron_variant	Intron 2 of 2	3		ENSP00000406781.1

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70860 AN: 151884 Hom.: 16974 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.467 AC: 70945 AN: 152002 Hom.: 17011 Cov.: 32 AF XY: 0.460 AC XY: 34209 AN XY: 74298

African (AFR) AF: 0.552 AC: 22877 AN: 41458

American (AMR) AF: 0.335 AC: 5121 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1605 AN: 5166

South Asian (SAS) AF: 0.450 AC: 2169 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4606 AN: 10566

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31710 AN: 67946

Other (OTH) AF: 0.449 AC: 948 AN: 2112

Alfa AF: 0.472 Hom.: 13294

Bravo AF: 0.460

Asia WGS AF: 0.402 AC: 1399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.035
DANN	Benign	0.30
PhyloP100		-1.5
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: rs10794030; hg19: chr10-127562375;