chr15-42292791-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_198141.3(GANC):c.386A>G(p.Asp129Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_198141.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GANC | NM_198141.3 | c.386A>G | p.Asp129Gly | missense_variant | 5/24 | ENST00000318010.13 | |
GANC | NM_001393928.1 | c.386A>G | p.Asp129Gly | missense_variant | 6/25 | ||
GANC | NM_001393929.1 | c.386A>G | p.Asp129Gly | missense_variant | 6/25 | ||
GANC | NM_001301409.2 | c.386A>G | p.Asp129Gly | missense_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GANC | ENST00000318010.13 | c.386A>G | p.Asp129Gly | missense_variant | 5/24 | 1 | NM_198141.3 | P1 | |
GANC | ENST00000566442.5 | c.386A>G | p.Asp129Gly | missense_variant | 6/12 | 2 | |||
GANC | ENST00000562859.5 | c.386A>G | p.Asp129Gly | missense_variant | 6/6 | 5 | |||
GANC | ENST00000567421.1 | n.359A>G | non_coding_transcript_exon_variant | 4/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD4 exome Cov.: 33
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | 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