Variant chr6-30893223-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001297654.2(DDR1):c.1196-49C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 1,592,636 control chromosomes in the GnomAD database, including 92,123 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 0.28 ( 6843 hom., cov: 33)

Exomes 𝑓: 0.34 ( 85280 hom. )

Consequence

DDR1
NM_001297654.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.490

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DDR1	NM_001297654.2 linkuse as main transcript	c.1196-49C>T		intron_variant		ENST00000376568.8	NP_001284583.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DDR1	ENST00000376568.8 linkuse as main transcript	c.1196-49C>T		intron_variant		1	NM_001297654.2	ENSP00000365752	P1	Q08345-1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42582

AN:

152084

Hom.:

6845

Cov.:

show subpopulations

Gnomad AFR

AF:

0.125

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.391

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.393

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.315

AC:

74164

AN:

235212

Hom.:

12458

AF XY:

0.324

AC XY:

41371

AN XY:

127820

show subpopulations

Gnomad AFR exome

AF:

0.119

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.375

Gnomad EAS exome

AF:

0.285

Gnomad SAS exome

AF:

0.280

Gnomad FIN exome

AF:

0.399

Gnomad NFE exome

AF:

0.371

Gnomad OTH exome

AF:

0.336

GnomAD4 exome

AF:

0.339

AC:

488467

AN:

1440434

Hom.:

85280

Cov.:

AF XY:

0.339

AC XY:

242475

AN XY:

715360

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.220

Gnomad4 ASJ exome

AF:

0.365

Gnomad4 EAS exome

AF:

0.242

Gnomad4 SAS exome

AF:

0.280

Gnomad4 FIN exome

AF:

0.387

Gnomad4 NFE exome

AF:

0.358

Gnomad4 OTH exome

AF:

0.311

GnomAD4 genome

AF:

0.280

AC:

42591

AN:

152202

Hom.:

6843

Cov.:

AF XY:

0.281

AC XY:

20911

AN XY:

74392

show subpopulations

Gnomad4 AFR

AF:

0.125

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.391

Gnomad4 EAS

AF:

0.256

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.393

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.279

Alfa

AF:

0.337

Hom.:

3045

Bravo

AF:

0.263

Asia WGS

AF:

0.214

AC:

748

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.4

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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