6-30900456-G-C

Variant names:

• chr6-30900456-G-C
• rs9468844
• ENST00000908927.1:c.*1160G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000908927.1(DDR1):​c.*1160G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,024 control chromosomes in the GnomAD database, including 6,047 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 0.26 (6047 hom., cov: 32)
• Consequence: DDR1 ENST00000908927.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 4 publications found

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 Gene-Disease associations (from GenCC):

• chondrodysplasia

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000908927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DDR1	ENST00000908927.1		c.*1160G>C		3_prime_UTR	Exon 18 of 18	ENSP00000578986.1
	DDR1	ENST00000908924.1		c.*1160G>C		3_prime_UTR	Exon 19 of 19	ENSP00000578983.1
	DDR1	ENST00000908949.1		c.*1160G>C		3_prime_UTR	Exon 17 of 17	ENSP00000579008.1

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39533 AN: 151906 Hom.: 6033 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.260 AC: 39569 AN: 152024 Hom.: 6047 Cov.: 32 AF XY: 0.271 AC XY: 20104 AN XY: 74290

African (AFR) AF: 0.271 AC: 11225 AN: 41432

American (AMR) AF: 0.368 AC: 5620 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 923 AN: 3472

East Asian (EAS) AF: 0.606 AC: 3137 AN: 5174

South Asian (SAS) AF: 0.509 AC: 2449 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2710 AN: 10556

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12612 AN: 67982

Other (OTH) AF: 0.263 AC: 555 AN: 2108

Alfa AF: 0.110 Hom.: 205

Bravo AF: 0.266

Asia WGS AF: 0.546 AC: 1896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.5
DANN	Benign	0.61
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9468844; hg19: chr6-30868233;