19-3902504-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.95C>T(p.Thr32Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000386 in 1,579,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. T32T) has been classified as Likely benign.
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.95C>T | p.Thr32Met | missense_variant | Exon 3 of 13 | ENST00000450849.7 | NP_149053.1 | |
ATCAY | XM_047439578.1 | c.-293C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 12 | XP_047295534.1 | |||
ATCAY | XM_047439578.1 | c.-293C>T | 5_prime_UTR_variant | Exon 2 of 12 | XP_047295534.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATCAY | ENST00000450849.7 | c.95C>T | p.Thr32Met | missense_variant | Exon 3 of 13 | 1 | NM_033064.5 | ENSP00000390941.1 | ||
ATCAY | ENST00000600960.1 | c.95C>T | p.Thr32Met | missense_variant | Exon 2 of 13 | 5 | ENSP00000470842.1 | |||
ATCAY | ENST00000598136.5 | c.95C>T | p.Thr32Met | missense_variant | Exon 4 of 5 | 4 | ENSP00000471731.1 | |||
ATCAY | ENST00000597739.1 | n.166C>T | non_coding_transcript_exon_variant | Exon 4 of 14 | 2 | ENSP00000472263.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000254 AC: 5AN: 197198Hom.: 0 AF XY: 0.0000283 AC XY: 3AN XY: 106152
GnomAD4 exome AF: 0.0000406 AC: 58AN: 1427848Hom.: 0 Cov.: 31 AF XY: 0.0000453 AC XY: 32AN XY: 707146
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at