17-40140769-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_007359.5(CASC3):c.221A>T(p.Glu74Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000941 in 1,169,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E74D) has been classified as Uncertain significance.
Frequency
Consequence
NM_007359.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASC3 | NM_007359.5 | c.221A>T | p.Glu74Val | missense_variant | Exon 1 of 14 | ENST00000264645.12 | NP_031385.2 | |
CASC3 | XM_005257163.3 | c.221A>T | p.Glu74Val | missense_variant | Exon 1 of 14 | XP_005257220.1 | ||
CASC3 | XM_047435623.1 | c.221A>T | p.Glu74Val | missense_variant | Exon 1 of 9 | XP_047291579.1 | ||
CASC3 | XM_047435624.1 | c.-745A>T | 5_prime_UTR_variant | Exon 1 of 15 | XP_047291580.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000101 AC: 10AN: 99416Hom.: 0 Cov.: 24
GnomAD3 exomes AF: 0.0000378 AC: 3AN: 79392Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 42364
GnomAD4 exome AF: 0.0000935 AC: 100AN: 1070082Hom.: 0 Cov.: 33 AF XY: 0.0000927 AC XY: 48AN XY: 517712
GnomAD4 genome AF: 0.000101 AC: 10AN: 99416Hom.: 0 Cov.: 24 AF XY: 0.0000437 AC XY: 2AN XY: 45770
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at