18-24155724-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_153769.3(CABYR):c.223A>T(p.Thr75Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000825 in 1,453,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_153769.3 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CABYR | NM_153769.3 | c.223A>T | p.Thr75Ser | missense_variant | 4/6 | ENST00000399496.8 | NP_722453.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CABYR | ENST00000399496.8 | c.223A>T | p.Thr75Ser | missense_variant | 4/6 | 1 | NM_153769.3 | ENSP00000382419 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244374Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132118
GnomAD4 exome AF: 0.00000825 AC: 12AN: 1453708Hom.: 0 Cov.: 31 AF XY: 0.0000111 AC XY: 8AN XY: 722634
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 13, 2022 | The c.223A>T (p.T75S) alteration is located in exon 4 (coding exon 3) of the CABYR gene. This alteration results from a A to T substitution at nucleotide position 223, causing the threonine (T) at amino acid position 75 to be replaced by a serine (S). 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