Variant chr6-30897427-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001297654.2(DDR1):c.2046A>C(p.Pro682=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 1,613,914 control chromosomes in the GnomAD database, including 33,041 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 0.19 ( 3158 hom., cov: 32)

Exomes 𝑓: 0.18 ( 29883 hom. )

Consequence

DDR1
NM_001297654.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP7

Synonymous conserved (PhyloP=-1.76 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.385 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.2046A>C	p.Pro682=	synonymous_variant	15/18	ENST00000376568.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DDR1	ENST00000376568.8 linkuse as main transcript	c.2046A>C	p.Pro682=	synonymous_variant	15/18	1	NM_001297654.2	P1	Q08345-1

Frequencies

GnomAD3 genomes

AF:

0.186

AC:

28275

AN:

151982

Hom.:

3143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.293

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.372

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.156

Gnomad OTH

AF:

0.181

GnomAD3 exomes

AF:

0.239

AC:

60012

AN:

251390

Hom.:

8807

AF XY:

0.240

AC XY:

32604

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.130

Gnomad AMR exome

AF:

0.396

Gnomad ASJ exome

AF:

0.207

Gnomad EAS exome

AF:

0.340

Gnomad SAS exome

AF:

0.384

Gnomad FIN exome

AF:

0.222

Gnomad NFE exome

AF:

0.159

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.184

AC:

268268

AN:

1461814

Hom.:

29883

Cov.:

AF XY:

0.189

AC XY:

137115

AN XY:

727206

show subpopulations

Gnomad4 AFR exome

AF:

0.126

Gnomad4 AMR exome

AF:

0.386

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.411

Gnomad4 SAS exome

AF:

0.379

Gnomad4 FIN exome

AF:

0.224

Gnomad4 NFE exome

AF:

0.150

Gnomad4 OTH exome

AF:

0.208

GnomAD4 genome

AF:

0.186

AC:

28308

AN:

152100

Hom.:

3158

Cov.:

AF XY:

0.196

AC XY:

14535

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.132

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.203

Gnomad4 EAS

AF:

0.373

Gnomad4 SAS

AF:

0.400

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.156

Gnomad4 OTH

AF:

0.189

Alfa

AF:

0.163

Hom.:

948

Bravo

AF:

0.185

Asia WGS

AF:

0.441

AC:

1530

AN:

3478

EpiCase

AF:

0.155

EpiControl

AF:

0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

5.2

DANN

Benign

0.59

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