17-40163707-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_007359.5(CASC3):c.1012C>T(p.Arg338Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007359.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASC3 | NM_007359.5 | c.1012C>T | p.Arg338Trp | missense_variant | 7/14 | ENST00000264645.12 | |
CASC3 | XM_005257163.3 | c.1012C>T | p.Arg338Trp | missense_variant | 7/14 | ||
CASC3 | XM_047435623.1 | c.1012C>T | p.Arg338Trp | missense_variant | 7/9 | ||
CASC3 | XM_047435624.1 | c.94C>T | p.Arg32Trp | missense_variant | 8/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASC3 | ENST00000264645.12 | c.1012C>T | p.Arg338Trp | missense_variant | 7/14 | 1 | NM_007359.5 | P1 | |
CASC3 | ENST00000418132.7 | n.1243C>T | non_coding_transcript_exon_variant | 7/8 | 1 | ||||
CASC3 | ENST00000474190.1 | c.566+105C>T | intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152070Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251442Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135896
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727246
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74400
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at