1-162773628-G-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006182.4(DDR2):c.1856+32G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.999 in 1,612,978 control chromosomes in the GnomAD database, including 805,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 1.0 ( 75527 hom., cov: 32)
Exomes 𝑓: 1.0 ( 729694 hom. )
Consequence
DDR2
NM_006182.4 intron
NM_006182.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.33
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 1-162773628-G-T is Benign according to our data. Variant chr1-162773628-G-T is described in ClinVar as [Benign]. Clinvar id is 259932.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DDR2 | NM_006182.4 | c.1856+32G>T | intron_variant | ENST00000367921.8 | NP_006173.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DDR2 | ENST00000367921.8 | c.1856+32G>T | intron_variant | 1 | NM_006182.4 | ENSP00000356898.3 | ||||
DDR2 | ENST00000367922.7 | c.1856+32G>T | intron_variant | 1 | ENSP00000356899.2 | |||||
DDR2 | ENST00000446985.6 | c.1856+32G>T | intron_variant | 3 | ENSP00000400309.2 |
Frequencies
GnomAD3 genomes AF: 0.996 AC: 151583AN: 152236Hom.: 75468 Cov.: 32
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GnomAD3 exomes AF: 0.999 AC: 250863AN: 251134Hom.: 125299 AF XY: 0.999 AC XY: 135608AN XY: 135732
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GnomAD4 exome AF: 1.00 AC: 1460003AN: 1460624Hom.: 729694 Cov.: 51 AF XY: 1.00 AC XY: 726367AN XY: 726646
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GnomAD4 genome AF: 0.996 AC: 151701AN: 152354Hom.: 75527 Cov.: 32 AF XY: 0.996 AC XY: 74176AN XY: 74494
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ClinVar
Significance: Benign
Submissions summary: Uncertain:1Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 12, 2019 | - - |
Squamous cell lung carcinoma Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing;in vivo | Faculté Pluridciplinaire Nador, Université Mohamed Premier | May 05, 2020 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Warburg-cinotti syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 16
Find out detailed SpliceAI scores and Pangolin per-transcript scores at