3-126542213-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152889.3(CHST13):c.661C>T(p.His221Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000226 in 1,461,010 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H221Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_152889.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000595 AC: 9AN: 151342Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000327 AC: 3AN: 91828Hom.: 0 AF XY: 0.0000186 AC XY: 1AN XY: 53832
GnomAD4 exome AF: 0.0000183 AC: 24AN: 1309560Hom.: 0 Cov.: 34 AF XY: 0.0000217 AC XY: 14AN XY: 646592
GnomAD4 genome AF: 0.0000594 AC: 9AN: 151450Hom.: 0 Cov.: 33 AF XY: 0.0000676 AC XY: 5AN XY: 74014
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.661C>T (p.H221Y) alteration is located in exon 3 (coding exon 3) of the CHST13 gene. This alteration results from a C to T substitution at nucleotide position 661, causing the histidine (H) at amino acid position 221 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