4-168488807-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505150.5. 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
	DDX60L	ENST00000505150.5	TSL:5	n.601+1551A>G		intron	N/A
	ENSG00000298211	ENST00000753908.1		n.417+742T>C		intron	N/A

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

African (AFR) AF: 0.808 AC: 33533 AN: 41518

American (AMR) AF: 0.824 AC: 12612 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2903 AN: 3472

East Asian (EAS) AF: 0.877 AC: 4544 AN: 5180

South Asian (SAS) AF: 0.855 AC: 4126 AN: 4828

European-Finnish (FIN) AF: 0.878 AC: 9306 AN: 10598

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55992 AN: 68040

Other (OTH) AF: 0.818 AC: 1728 AN: 2112

Alfa AF: 0.823 Hom.: 174719

Bravo AF: 0.820

Asia WGS AF: 0.858 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0020
DANN	Benign	0.51
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs2710833; hg19: chr4-169409958;