rs6819953

Positions:

• chr4-168493278-G-T

Variant summary

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

The ENST00000512958.1(DDX60L):​n.238-393C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 152,210 control chromosomes in the GnomAD database, including 735 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 0.092 (735 hom., cov: 32)
• Consequence: DDX60L ENST00000512958.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

Genes affected

DDX60L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986198	XR_001741448.3	n.281-393C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX60L	ENST00000505150.5	n.289-393C>A		intron_variant		5
DDX60L	ENST00000512958.1	n.238-393C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0919 AC: 13977 AN: 152092 Hom.: 734 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0554

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.0307

Gnomad SAS AF: 0.0575

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0817

Gnomad OTH AF: 0.0836

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

GnomAD4 genome AF: 0.0919 AC: 13993 AN: 152210 Hom.: 735 Cov.: 32 AF XY: 0.0939 AC XY: 6991 AN XY: 74426

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0554

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.0307

Gnomad4 SAS AF: 0.0584

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.0817

Gnomad4 OTH AF: 0.0827

Alfa AF: 0.0804 Hom.: 751

Bravo AF: 0.0865

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6819953; hg19: chr4-169414429;