16-61817615-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000577390.6(CDH8):c.1141G>A(p.Val381Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000651 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000577390.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDH8 | NM_001796.5 | c.1141G>A | p.Val381Met | missense_variant | 7/12 | ENST00000577390.6 | NP_001787.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDH8 | ENST00000577390.6 | c.1141G>A | p.Val381Met | missense_variant | 7/12 | 1 | NM_001796.5 | ENSP00000462701 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251212Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135766
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461798Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727188
GnomAD4 genome AF: 0.000118 AC: 18AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.1141G>A (p.V381M) alteration is located in exon 7 (coding exon 6) of the CDH8 gene. This alteration results from a G to A substitution at nucleotide position 1141, causing the valine (V) at amino acid position 381 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at