chr19-1912106-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138422.4(ADAT3):c.59C>T(p.Ala20Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000029 in 1,517,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_138422.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAT3 | NM_138422.4 | c.59C>T | p.Ala20Val | missense_variant | 2/2 | ENST00000329478.4 | NP_612431.2 | |
SCAMP4 | NM_079834.4 | c.-41-2873C>T | intron_variant | ENST00000316097.13 | NP_524558.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.59C>T | p.Ala20Val | missense_variant | 2/2 | 1 | NM_138422.4 | ENSP00000332448 | P1 | |
SCAMP4 | ENST00000316097.13 | c.-41-2873C>T | intron_variant | 1 | NM_079834.4 | ENSP00000316007 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152268Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000203 AC: 24AN: 118070Hom.: 0 AF XY: 0.000169 AC XY: 11AN XY: 65224
GnomAD4 exome AF: 0.0000293 AC: 40AN: 1365552Hom.: 0 Cov.: 30 AF XY: 0.0000327 AC XY: 22AN XY: 673046
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152268Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 17, 2016 | - - |
Intellectual disability-strabismus syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 05, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at