20-45883652-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_080603.5(ZSWIM1):c.1060C>T(p.His354Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000479 in 1,461,880 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H354Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_080603.5 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 |
---|---|---|---|---|---|---|---|---|
ZSWIM1 | NM_080603.5 | c.1060C>T | p.His354Tyr | missense_variant | Exon 2 of 2 | ENST00000372523.1 | NP_542170.3 | |
ZSWIM1 | XM_005260610.6 | c.1060C>T | p.His354Tyr | missense_variant | Exon 2 of 2 | XP_005260667.1 | ||
ZSWIM1 | XM_005260611.5 | c.1060C>T | p.His354Tyr | missense_variant | Exon 2 of 2 | XP_005260668.1 | ||
ZSWIM1 | XM_011529100.3 | c.1060C>T | p.His354Tyr | missense_variant | Exon 2 of 2 | XP_011527402.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251400Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135876
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461880Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727240
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1060C>T (p.H354Y) alteration is located in exon 2 (coding exon 1) of the ZSWIM1 gene. This alteration results from a C to T substitution at nucleotide position 1060, causing the histidine (H) at amino acid position 354 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