19-1912125-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138422.4(ADAT3):c.78G>T(p.Gln26His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000215 in 1,398,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADAT3 | NM_138422.4 | c.78G>T | p.Gln26His | missense_variant | 2/2 | ENST00000329478.4 | NP_612431.2 | |
SCAMP4 | NM_079834.4 | c.-41-2854G>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.78G>T | p.Gln26His | missense_variant | 2/2 | 1 | NM_138422.4 | ENSP00000332448 | P1 | |
SCAMP4 | ENST00000316097.13 | c.-41-2854G>T | intron_variant | 1 | NM_079834.4 | ENSP00000316007 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1398508Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 691620
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 07, 2022 | The c.30G>T (p.Q10H) alteration is located in exon 2 (coding exon 1) of the ADAT3 gene. This alteration results from a G to T substitution at nucleotide position 30, causing the glutamine (Q) at amino acid position 10 to be replaced by a histidine (H). 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