chr19-1912262-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_138422.4(ADAT3):c.215C>T(p.Thr72Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000314 in 1,594,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T72T) has been classified as Benign.
Frequency
Consequence
NM_138422.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAT3 | NM_138422.4 | c.215C>T | p.Thr72Ile | missense_variant | 2/2 | ENST00000329478.4 | |
SCAMP4 | NM_079834.4 | c.-41-2717C>T | intron_variant | ENST00000316097.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAT3 | ENST00000329478.4 | c.215C>T | p.Thr72Ile | missense_variant | 2/2 | 1 | NM_138422.4 | P1 | |
SCAMP4 | ENST00000316097.13 | c.-41-2717C>T | intron_variant | 1 | NM_079834.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000277 AC: 4AN: 1442518Hom.: 0 Cov.: 30 AF XY: 0.00000279 AC XY: 2AN XY: 716896
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152264Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74386
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.167C>T (p.T56I) alteration is located in exon 2 (coding exon 1) of the ADAT3 gene. This alteration results from a C to T substitution at nucleotide position 167, causing the threonine (T) at amino acid position 56 to be replaced by an isoleucine (I). 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