rs786201492
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004360.5(CDH1):c.114G>A(p.Thr38=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,398,836 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 (★★). Synonymous variant affecting the same amino acid position (i.e. T38T) has been classified as Likely benign.
Frequency
Consequence
NM_004360.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDH1 | NM_004360.5 | c.114G>A | p.Thr38= | synonymous_variant | 2/16 | ENST00000261769.10 | |
CDH1 | NM_001317184.2 | c.114G>A | p.Thr38= | synonymous_variant | 2/15 | ||
CDH1 | NM_001317185.2 | c.-1502G>A | 5_prime_UTR_variant | 2/16 | |||
CDH1 | NM_001317186.2 | c.-1706G>A | 5_prime_UTR_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.114G>A | p.Thr38= | synonymous_variant | 2/16 | 1 | NM_004360.5 | P1 | |
CDH1 | ENST00000422392.6 | c.114G>A | p.Thr38= | synonymous_variant | 2/15 | 1 | |||
CDH1 | ENST00000566612.5 | c.114G>A | p.Thr38= | synonymous_variant, NMD_transcript_variant | 2/15 | 1 | |||
CDH1 | ENST00000566510.5 | c.114G>A | p.Thr38= | synonymous_variant, NMD_transcript_variant | 2/15 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1398836Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1AN XY: 689922
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Oct 02, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 24, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Hereditary diffuse gastric adenocarcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at