rs770500546
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138422.4(ADAT3):c.104C>G(p.Pro35Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000849 in 1,414,126 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 (★).
Frequency
Consequence
NM_138422.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.104C>G | p.Pro35Arg | missense_variant | Exon 2 of 2 | 1 | NM_138422.4 | ENSP00000332448.2 | ||
SCAMP4 | ENST00000316097.13 | c.-41-2828C>G | intron_variant | Intron 1 of 6 | 1 | NM_079834.4 | ENSP00000316007.7 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD2 exomes AF: 0.0000298 AC: 5AN: 167976 AF XY: 0.0000108 show subpopulations
GnomAD4 exome AF: 0.00000849 AC: 12AN: 1414126Hom.: 0 Cov.: 30 AF XY: 0.00000857 AC XY: 6AN XY: 700384 show subpopulations
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
not provided Uncertain:1
In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at