4-168488807-T-C

Variant names:

• chr4-168488807-T-C
• rs2710833
• XR_001741448.3:n.1095A>G

Variant summary

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

The XR_001741448.3(LOC107986198):​n.1095A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,258 control chromosomes in the GnomAD database, including 52,017 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 0.83 (52017 hom., cov: 33)
• Consequence: LOC107986198 XR_001741448.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40

Genes affected

LOC107986198 (HGNC:):

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 = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986198	XR_001741448.3	n.1095A>G		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DDX60L	ENST00000505150.5	n.601+1551A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125713 AN: 152140 Hom.: 51982 Cov.: 33

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.817

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

GnomAD4 genome AF: 0.826 AC: 125805 AN: 152258 Hom.: 52017 Cov.: 33 AF XY: 0.829 AC XY: 61756 AN XY: 74456

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.836

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.818

Alfa AF: 0.826 Hom.: 77662

Bravo AF: 0.820

Asia WGS AF: 0.858 AC: 2985 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	0.0020
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2710833; hg19: chr4-169409958;