rs10517053

Variant names:

• chr4-24524749-G-A
• rs10517053
• ENST00000510645.5:n.258+4852C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-24524749-G-A
• chr4-24524749-G-C
• chr4-24524749-G-T

Variant summary

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

The ENST00000510645.5(DHX15):​n.258+4852C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,034 control chromosomes in the GnomAD database, including 29,956 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 0.62 (29956 hom., cov: 32)
• Consequence: DHX15 ENST00000510645.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

DHX15 (HGNC:2738): (DEAH-box helicase 15) The protein encoded by this gene is a putative ATP-dependent RNA helicase implicated in pre-mRNA splicing. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DHX15	ENST00000510645.5	n.258+4852C>T		intron_variant	Intron 2 of 2	5

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94926 AN: 151916 Hom.: 29930 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.625 AC: 95000 AN: 152034 Hom.: 29956 Cov.: 32 AF XY: 0.618 AC XY: 45955 AN XY: 74308

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.606

Alfa AF: 0.629 Hom.: 9399

Bravo AF: 0.620

Asia WGS AF: 0.618 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517053; hg19: chr4-24526372;