6-30891471-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001297654.2(DDR1):c.657C>T(p.Thr219Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000993 in 1,612,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000082 ( 0 hom. )
Consequence
DDR1
NM_001297654.2 synonymous
NM_001297654.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -6.11
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.62).
BP6
Variant 6-30891471-C-T is Benign according to our data. Variant chr6-30891471-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3772532.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-6.11 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDR1 | NM_001297654.2 | c.657C>T | p.Thr219Thr | synonymous_variant | Exon 6 of 18 | ENST00000376568.8 | NP_001284583.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151658Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000284 AC: 7AN: 246180Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134228
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GnomAD4 exome AF: 0.00000822 AC: 12AN: 1460384Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726532
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GnomAD4 genome AF: 0.0000264 AC: 4AN: 151658Hom.: 0 Cov.: 32 AF XY: 0.0000405 AC XY: 3AN XY: 74012
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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
Feb 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
DDR1: BP4, BP7 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at