rs1963569

chr4-168417369-A-Cchr4-168417369-A-T

Variant summary

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

The NM_001012967.3(DDX60L):c.2611-572T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,948 control chromosomes in the GnomAD database, including 17,391 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 0.46 (17391 hom., cov: 31)
• Consequence: DDX60L NM_001012967.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

DDX60L (HGNC:26429): (DExD/H-box 60 like) This gene encodes a member of the DExD/H-box helicase family of proteins, a subset of the super family 2 helicases. Members of the DExD/H-box helicase family share a conserved functional core comprised of two RecA-like globular domains. These domains contain conserved motifs that mediate ATP binding, ATP hydrolysis, nucleic acid binding, and RNA unwinding. In addition to functions in RNA metabolism, members of this family are involved in anti-viral immunity and act as cytosolic sensors of viral nucleic acids. The protein encoded by this gene has been shown to inhibit hepatitis C virus replication in response to interferon stimulation in cell culture. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDX60L	NM_001012967.3	c.2611-572T>G		intron_variant		ENST00000682922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDX60L	ENST00000682922.1	c.2611-572T>G		intron_variant			NM_001012967.3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70332 AN: 151830 Hom.: 17389 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.463 AC: 70357 AN: 151948 Hom.: 17391 Cov.: 31 AF XY: 0.464 AC XY: 34446 AN XY: 74284

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.519

Alfa AF: 0.515 Hom.: 19206

Bravo AF: 0.466

Asia WGS AF: 0.641 AC: 2230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.6
Dann	Benign	0.71

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

Other links and lift over

dbSNP: rs1963569; hg19: chr4-169338520;