Variant rs1049623 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001297654.2(DDR1):c.1908T>C(p.Val636=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 1,613,196 control chromosomes in the GnomAD database, including 148,378 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 0.44 ( 14867 hom., cov: 29)

Exomes 𝑓: 0.42 ( 133511 hom. )

Consequence

DDR1
NM_001297654.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.582

Variant links:

Genes affected

DDR1 (HGNC:2730): (discoidin domain receptor tyrosine kinase 1) Receptor tyrosine kinases play a key role in the communication of cells with their microenvironment. These kinases are involved in the regulation of cell growth, differentiation and metabolism. The protein encoded by this gene belongs to a subfamily of tyrosine kinase receptors with homology to Dictyostelium discoideum protein discoidin I in their extracellular domain, and that are activated by various types of collagen. Expression of this protein is restricted to epithelial cells, particularly in the kidney, lung, gastrointestinal tract, and brain. In addition, it has been shown to be significantly overexpressed in several human tumors. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

DDR1 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=-0.45).

BP7

Synonymous conserved (PhyloP=0.582 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DDR1	NM_001297654.2 linkuse as main transcript	c.1908T>C	p.Val636=	synonymous_variant	14/18	ENST00000376568.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDR1	ENST00000376568.8 linkuse as main transcript	c.1908T>C	p.Val636=	synonymous_variant	14/18	1	NM_001297654.2	P1	Q08345-1

Frequencies

GnomAD3 genomes

AF:

0.435

AC:

65938

AN:

151524

Hom.:

14830

Cov.:

show subpopulations

Gnomad AFR

AF:

0.457

Gnomad AMI

AF:

0.525

Gnomad AMR

AF:

0.489

Gnomad ASJ

AF:

0.401

Gnomad EAS

AF:

0.682

Gnomad SAS

AF:

0.637

Gnomad FIN

AF:

0.396

Gnomad MID

AF:

0.329

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.402

GnomAD3 exomes

AF:

0.469

AC:

117984

AN:

251318

Hom.:

29541

AF XY:

0.469

AC XY:

63764

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.458

Gnomad AMR exome

AF:

0.593

Gnomad ASJ exome

AF:

0.413

Gnomad EAS exome

AF:

0.658

Gnomad SAS exome

AF:

0.620

Gnomad FIN exome

AF:

0.389

Gnomad NFE exome

AF:

0.385

Gnomad OTH exome

AF:

0.418

GnomAD4 exome

AF:

0.419

AC:

612437

AN:

1461554

Hom.:

133511

Cov.:

AF XY:

0.424

AC XY:

308397

AN XY:

727058

show subpopulations

Gnomad4 AFR exome

AF:

0.454

Gnomad4 AMR exome

AF:

0.581

Gnomad4 ASJ exome

AF:

0.419

Gnomad4 EAS exome

AF:

0.647

Gnomad4 SAS exome

AF:

0.615

Gnomad4 FIN exome

AF:

0.395

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.447

GnomAD4 genome

AF:

0.435

AC:

66028

AN:

151642

Hom.:

14867

Cov.:

AF XY:

0.441

AC XY:

32635

AN XY:

74078

show subpopulations

Gnomad4 AFR

AF:

0.458

Gnomad4 AMR

AF:

0.489

Gnomad4 ASJ

AF:

0.401

Gnomad4 EAS

AF:

0.683

Gnomad4 SAS

AF:

0.638

Gnomad4 FIN

AF:

0.396

Gnomad4 NFE

AF:

0.385

Gnomad4 OTH

AF:

0.408

Alfa

AF:

0.401

Hom.:

24585

Bravo

AF:

0.441

Asia WGS

AF:

0.670

AC:

2328

AN:

3478

EpiCase

AF:

0.385

EpiControl

AF:

0.385

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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