chr18-27952177-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000269141.8(CDH2):c.2697C>T(p.Asp899=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000137 in 1,461,388 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: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
CDH2
ENST00000269141.8 synonymous
ENST00000269141.8 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.85
Genes affected
CDH2 (HGNC:1759): (cadherin 2) This gene encodes a classical cadherin and member of the cadherin superfamily. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein is proteolytically processed to generate a calcium-dependent cell adhesion molecule and glycoprotein. This protein plays a role in the establishment of left-right asymmetry, development of the nervous system and the formation of cartilage and bone. [provided by RefSeq, Nov 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 18-27952177-G-A is Benign according to our data. Variant chr18-27952177-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2790390.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH2 | NM_001792.5 | c.2697C>T | p.Asp899= | synonymous_variant | 16/16 | ENST00000269141.8 | NP_001783.2 | |
CDH2 | NM_001308176.2 | c.2604C>T | p.Asp868= | synonymous_variant | 15/15 | NP_001295105.1 | ||
CDH2 | XM_011525788.1 | c.2442C>T | p.Asp814= | synonymous_variant | 16/16 | XP_011524090.1 | ||
CDH2 | XM_017025514.3 | c.2514+11180C>T | intron_variant | XP_016881003.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH2 | ENST00000269141.8 | c.2697C>T | p.Asp899= | synonymous_variant | 16/16 | 1 | NM_001792.5 | ENSP00000269141 | P1 | |
ENST00000423367.2 | n.199-2341G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251224Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135776
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461388Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727014
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GnomAD4 genome Cov.: 32
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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 | Labcorp Genetics (formerly Invitae), Labcorp | Dec 09, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at