chr4-24524749-G-A

Variant names:

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

Variant summary

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

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510645.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DHX15	ENST00000510645.5	TSL:5	n.258+4852C>T		intron	N/A

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

African (AFR) AF: 0.622 AC: 25808 AN: 41462

American (AMR) AF: 0.522 AC: 7972 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1836 AN: 3462

East Asian (EAS) AF: 0.677 AC: 3504 AN: 5172

South Asian (SAS) AF: 0.515 AC: 2485 AN: 4822

European-Finnish (FIN) AF: 0.643 AC: 6788 AN: 10554

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44458 AN: 67968

Other (OTH) AF: 0.606 AC: 1280 AN: 2112

Alfa AF: 0.630 Hom.: 11850

Bravo AF: 0.620

Asia WGS AF: 0.618 AC: 2148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs10517053; hg19: chr4-24526372;