chr1-10639009-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001079843.3(CASZ1):c.5213C>G(p.Pro1738Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0464 in 991,076 control chromosomes in the GnomAD database, including 1,578 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001079843.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASZ1 | NM_001079843.3 | c.5213C>G | p.Pro1738Arg | missense_variant | 21/21 | ENST00000377022.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASZ1 | ENST00000377022.8 | c.5213C>G | p.Pro1738Arg | missense_variant | 21/21 | 1 | NM_001079843.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0698 AC: 10168AN: 145726Hom.: 606 Cov.: 32
GnomAD3 exomes AF: 0.0573 AC: 295AN: 5146Hom.: 23 AF XY: 0.0675 AC XY: 210AN XY: 3112
GnomAD4 exome AF: 0.0423 AC: 35775AN: 845302Hom.: 969 Cov.: 32 AF XY: 0.0425 AC XY: 16669AN XY: 392174
GnomAD4 genome ? AF: 0.0698 AC: 10173AN: 145774Hom.: 609 Cov.: 32 AF XY: 0.0681 AC XY: 4827AN XY: 70912
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at