chr16-68738384-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_004360.5(CDH1):c.136C>T(p.Leu46=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000258 in 1,550,554 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. L46L) 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.136C>T | p.Leu46= | synonymous_variant | 2/16 | ENST00000261769.10 | |
CDH1 | NM_001317184.2 | c.136C>T | p.Leu46= | synonymous_variant | 2/15 | ||
CDH1 | NM_001317185.2 | c.-1480C>T | 5_prime_UTR_variant | 2/16 | |||
CDH1 | NM_001317186.2 | c.-1684C>T | 5_prime_UTR_variant | 2/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDH1 | ENST00000261769.10 | c.136C>T | p.Leu46= | synonymous_variant | 2/16 | 1 | NM_004360.5 | P1 | |
CDH1 | ENST00000422392.6 | c.136C>T | p.Leu46= | synonymous_variant | 2/15 | 1 | |||
CDH1 | ENST00000566612.5 | c.136C>T | p.Leu46= | synonymous_variant, NMD_transcript_variant | 2/15 | 1 | |||
CDH1 | ENST00000566510.5 | c.136C>T | p.Leu46= | synonymous_variant, NMD_transcript_variant | 2/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000644 AC: 1AN: 155312Hom.: 0 AF XY: 0.0000122 AC XY: 1AN XY: 82114
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1398340Hom.: 0 Cov.: 31 AF XY: 0.00000435 AC XY: 3AN XY: 689652
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
Hereditary diffuse gastric adenocarcinoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 10, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jun 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at