10-133267956-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000415217.7(ADAM8):c.2059G>A(p.Gly687Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000222 in 1,260,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000415217.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAM8 | NM_001109.5 | c.2226G>A | p.Ser742= | synonymous_variant | 20/23 | ENST00000445355.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM8 | ENST00000415217.7 | c.2059G>A | p.Gly687Ser | missense_variant | 19/22 | 1 | A2 | ||
ADAM8 | ENST00000445355.8 | c.2226G>A | p.Ser742= | synonymous_variant | 20/23 | 1 | NM_001109.5 | P2 | |
ADAM8 | ENST00000485491.6 | c.2031G>A | p.Ser677= | synonymous_variant | 18/20 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000363 AC: 1AN: 27578Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 14662
GnomAD4 exome AF: 0.0000162 AC: 18AN: 1108470Hom.: 0 Cov.: 31 AF XY: 0.0000133 AC XY: 7AN XY: 524974
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74474
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at