chr19-1912109-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138422.4(ADAT3):āc.62C>Gā(p.Pro21Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000731 in 1,368,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138422.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAT3 | NM_138422.4 | c.62C>G | p.Pro21Arg | missense_variant | 2/2 | ENST00000329478.4 | NP_612431.2 | |
SCAMP4 | NM_079834.4 | c.-41-2870C>G | intron_variant | ENST00000316097.13 | NP_524558.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.62C>G | p.Pro21Arg | missense_variant | 2/2 | 1 | NM_138422.4 | ENSP00000332448 | P1 | |
SCAMP4 | ENST00000316097.13 | c.-41-2870C>G | intron_variant | 1 | NM_079834.4 | ENSP00000316007 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 7.31e-7 AC: 1AN: 1368664Hom.: 0 Cov.: 30 AF XY: 0.00000148 AC XY: 1AN XY: 674794
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 18, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at