20-20052354-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016652.6(CRNKL1):āc.472A>Gā(p.Thr158Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,613,646 control chromosomes in the GnomAD database, including 190,825 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016652.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRNKL1 | NM_001278628.2 | c.-12A>G | 5_prime_UTR_variant | 1/14 | ENST00000536226.2 | NP_001265557.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRNKL1 | ENST00000536226.2 | c.-12A>G | 5_prime_UTR_variant | 1/14 | 1 | NM_001278628.2 | ENSP00000440733.1 |
Frequencies
GnomAD3 genomes AF: 0.484 AC: 73616AN: 151996Hom.: 18111 Cov.: 33
GnomAD3 exomes AF: 0.513 AC: 128806AN: 250868Hom.: 33849 AF XY: 0.506 AC XY: 68723AN XY: 135714
GnomAD4 exome AF: 0.484 AC: 707382AN: 1461532Hom.: 172696 Cov.: 68 AF XY: 0.483 AC XY: 351355AN XY: 727090
GnomAD4 genome AF: 0.484 AC: 73687AN: 152114Hom.: 18129 Cov.: 33 AF XY: 0.486 AC XY: 36115AN XY: 74366
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at