chr19-5739326-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152784.4(CATSPERD):c.460C>T(p.His154Tyr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000668 in 1,423,016 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152784.4 missense, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000353 AC: 53AN: 150332Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000736 AC: 17AN: 231000Hom.: 0 AF XY: 0.0000636 AC XY: 8AN XY: 125768
GnomAD4 exome AF: 0.0000330 AC: 42AN: 1272570Hom.: 0 Cov.: 20 AF XY: 0.0000405 AC XY: 26AN XY: 642044
GnomAD4 genome AF: 0.000352 AC: 53AN: 150446Hom.: 0 Cov.: 31 AF XY: 0.000313 AC XY: 23AN XY: 73418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.460C>T (p.H154Y) alteration is located in exon 7 (coding exon 7) of the CATSPERD gene. This alteration results from a C to T substitution at nucleotide position 460, causing the histidine (H) at amino acid position 154 to be replaced by a tyrosine (Y). 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