Variant chr2-15607269-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_004939.3(DDX1):c.912C>T(p.Asn304Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 1,609,522 control chromosomes in the GnomAD database, including 301,706 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 0.66 ( 34087 hom., cov: 32)

Exomes 𝑓: 0.60 ( 267619 hom. )

Consequence

DDX1
NM_004939.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.700

Variant links:

Genes affected

DDX1 (HGNC:2734): (DEAD-box helicase 1) DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein that acts as an ATP-dependent RNA helicase that has been found to promote coronaviruses replication. [provided by RefSeq, Aug 2021]

DDX1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP7

Synonymous conserved (PhyloP=0.7 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDX1	NM_004939.3 link	c.912C>T	p.Asn304Asn	synonymous_variant	13/26	ENST00000233084.8	NP_004930.1	Q92499-1A3RJH1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDX1	ENST00000233084.8 link	c.912C>T	p.Asn304Asn	synonymous_variant	13/26	1	NM_004939.3	ENSP00000233084.3		Q92499-1

Frequencies

GnomAD3 genomes

AF:

0.659

AC:

100103

AN:

151886

Hom.:

34051

Cov.:

show subpopulations

Gnomad AFR

AF:

0.809

Gnomad AMI

AF:

0.611

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.581

Gnomad EAS

AF:

0.886

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.596

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.622

GnomAD3 exomes

AF:

0.640

AC:

160845

AN:

251326

Hom.:

52981

AF XY:

0.634

AC XY:

86189

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.817

Gnomad AMR exome

AF:

0.677

Gnomad ASJ exome

AF:

0.573

Gnomad EAS exome

AF:

0.886

Gnomad SAS exome

AF:

0.724

Gnomad FIN exome

AF:

0.532

Gnomad NFE exome

AF:

0.570

Gnomad OTH exome

AF:

0.602

GnomAD4 exome

AF:

0.600

AC:

875049

AN:

1457518

Hom.:

267619

Cov.:

AF XY:

0.603

AC XY:

437527

AN XY:

725336

show subpopulations

Gnomad4 AFR exome

AF:

0.816

Gnomad4 AMR exome

AF:

0.669

Gnomad4 ASJ exome

AF:

0.572

Gnomad4 EAS exome

AF:

0.916

Gnomad4 SAS exome

AF:

0.720

Gnomad4 FIN exome

AF:

0.532

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.620

GnomAD4 genome

AF:

0.659

AC:

100201

AN:

152004

Hom.:

34087

Cov.:

AF XY:

0.660

AC XY:

49053

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.809

Gnomad4 AMR

AF:

0.657

Gnomad4 ASJ

AF:

0.581

Gnomad4 EAS

AF:

0.887

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.624

Alfa

AF:

0.606

Hom.:

15119

Bravo

AF:

0.673

Asia WGS

AF:

0.828

AC:

2879

AN:

3478

EpiCase

AF:

0.569

EpiControl

AF:

0.563

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

6.8

DANN

Benign

0.65

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over