chr10-125873806-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000284690.4(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
ENST00000284690.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.52
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons MANE Protein UniProt
DHX32NM_018180.3 linkuse as main transcriptc.283-6623G>A intron_variant ENST00000284690.4 NP_060650.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DHX32ENST00000284690.4 linkuse as main transcriptc.283-6623G>A intron_variant 1 NM_018180.3 ENSP00000284690 P1Q7L7V1-1
DHX32ENST00000415732.1 linkuse as main transcriptc.283-6623G>A intron_variant 3 ENSP00000406781

Frequencies

GnomAD3 genomes
AF:
0.467
AC:
70860
AN:
151884
Hom.:
16974
Cov.:
32
show subpopulations
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
show subpopulations
Gnomad4 AFR
AF:
0.552
Gnomad4 AMR
AF:
0.335
Gnomad4 ASJ
AF:
0.401
Gnomad4 EAS
AF:
0.311
Gnomad4 SAS
AF:
0.450
Gnomad4 FIN
AF:
0.436
Gnomad4 NFE
AF:
0.467
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.465
Hom.:
7799
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

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs10794030; hg19: chr10-127562375; API