1-162718891-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006182.4(DDR2):c.-27-146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00504 in 737,654 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0077 ( 19 hom., cov: 32)
Exomes 𝑓: 0.0044 ( 43 hom. )
Consequence
DDR2
NM_006182.4 intron
NM_006182.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.36
Genes affected
DDR2 (HGNC:2731): (discoidin domain receptor tyrosine kinase 2) This gene encodes a member of the discoidin domain receptor subclass of the receptor tyrosine kinase (RTKs) protein family. RTKs play a key role in the communication of cells with their microenvironment. The encoded protein is a collagen-induced receptor that activates signal transduction pathways involved in cell adhesion, proliferation, and extracellular matrix remodeling. This protein is expressed in numerous cell types and may alos be involved in wound repair and regulate tumor growth and invasiveness. Mutations in this gene are the cause of short limb-hand type spondylometaepiphyseal dysplasia. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 1-162718891-G-A is Benign according to our data. Variant chr1-162718891-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1219420.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00766 (1166/152296) while in subpopulation EAS AF= 0.0347 (180/5186). AF 95% confidence interval is 0.0306. There are 19 homozygotes in gnomad4. There are 557 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1158 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DDR2 | NM_006182.4 | c.-27-146G>A | intron_variant | ENST00000367921.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DDR2 | ENST00000367921.8 | c.-27-146G>A | intron_variant | 1 | NM_006182.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00761 AC: 1158AN: 152178Hom.: 18 Cov.: 32
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GnomAD4 exome AF: 0.00436 AC: 2555AN: 585358Hom.: 43 AF XY: 0.00433 AC XY: 1340AN XY: 309306
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GnomAD4 genome ? AF: 0.00766 AC: 1166AN: 152296Hom.: 19 Cov.: 32 AF XY: 0.00748 AC XY: 557AN XY: 74468
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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 | GeneDx | Dec 05, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at