19-3885778-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_033064.5(ATCAY):c.11C>T(p.Thr4Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000709 in 1,551,382 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 (★).
Frequency
Consequence
NM_033064.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATCAY | NM_033064.5 | c.11C>T | p.Thr4Ile | missense_variant | Exon 2 of 13 | ENST00000450849.7 | NP_149053.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152118Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.00000642 AC: 1AN: 155842Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82396
GnomAD4 exome AF: 0.00000572 AC: 8AN: 1399264Hom.: 0 Cov.: 31 AF XY: 0.00000580 AC XY: 4AN XY: 690180
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152118Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74288
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.11C>T (p.T4I) alteration is located in exon 2 (coding exon 1) of the ATCAY gene. This alteration results from a C to T substitution at nucleotide position 11, causing the threonine (T) at amino acid position 4 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