NM_138422.4:c.108G>T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_138422.4(ADAT3):c.108G>T(p.Glu36Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000918 in 1,568,450 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_138422.4 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.108G>T | p.Glu36Asp | missense_variant | Exon 2 of 2 | 1 | NM_138422.4 | ENSP00000332448.2 | ||
SCAMP4 | ENST00000316097.13 | c.-41-2824G>T | intron_variant | Intron 1 of 6 | 1 | NM_079834.4 | ENSP00000316007.7 |
Frequencies
GnomAD3 genomes AF: 0.0000722 AC: 11AN: 152270Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.000124 AC: 21AN: 169814 AF XY: 0.000107 show subpopulations
GnomAD4 exome AF: 0.0000939 AC: 133AN: 1416180Hom.: 0 Cov.: 30 AF XY: 0.000107 AC XY: 75AN XY: 701482 show subpopulations
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74394 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.60G>T (p.E20D) 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 60, causing the glutamic acid (E) at amino acid position 20 to be replaced by an aspartic acid (D). 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