chr19-1912487-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_138422.4(ADAT3):c.440G>A(p.Arg147Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000134 in 1,498,814 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_138422.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.440G>A | p.Arg147Gln | missense_variant | Exon 2 of 2 | 1 | NM_138422.4 | ENSP00000332448.2 | ||
SCAMP4 | ENST00000316097.13 | c.-41-2492G>A | intron_variant | Intron 1 of 6 | 1 | NM_079834.4 | ENSP00000316007.7 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152034Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000398 AC: 38AN: 95412Hom.: 0 AF XY: 0.000578 AC XY: 31AN XY: 53668
GnomAD4 exome AF: 0.000137 AC: 184AN: 1346672Hom.: 1 Cov.: 30 AF XY: 0.000199 AC XY: 132AN XY: 664194
GnomAD4 genome AF: 0.000112 AC: 17AN: 152142Hom.: 1 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74398
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
Intellectual disability-strabismus syndrome Uncertain:1
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Inborn genetic diseases Benign:1
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