chr6-30896706-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate
The NM_001297654.2(DDR1):c.1710C>T(p.Ala570=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000606 in 1,608,014 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00058 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00061 ( 4 hom. )
Consequence
DDR1
NM_001297654.2 synonymous
NM_001297654.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.908
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
BP6
?
Variant 6-30896706-C-T is Benign according to our data. Variant chr6-30896706-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2656344.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDR1 | NM_001297654.2 | c.1710C>T | p.Ala570= | synonymous_variant | 13/18 | ENST00000376568.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDR1 | ENST00000376568.8 | c.1710C>T | p.Ala570= | synonymous_variant | 13/18 | 1 | NM_001297654.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000585 AC: 89AN: 152108Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000978 AC: 237AN: 242424Hom.: 1 AF XY: 0.000924 AC XY: 121AN XY: 130984
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GnomAD4 exome AF: 0.000609 AC: 886AN: 1455788Hom.: 4 Cov.: 31 AF XY: 0.000637 AC XY: 461AN XY: 723970
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | DDR1: BS1 - |
Computational scores
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BayesDel_noAF
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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 25
Find out detailed SpliceAI scores and Pangolin per-transcript scores at