20-20039670-A-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001278628.2(CRNKL1):āc.1484T>Cā(p.Ile495Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001278628.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRNKL1 | NM_001278628.2 | c.1484T>C | p.Ile495Thr | missense_variant | 11/14 | ENST00000536226.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRNKL1 | ENST00000536226.2 | c.1484T>C | p.Ile495Thr | missense_variant | 11/14 | 1 | NM_001278628.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251426Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135882
GnomAD4 exome AF: 0.000116 AC: 170AN: 1461882Hom.: 0 Cov.: 32 AF XY: 0.000122 AC XY: 89AN XY: 727238
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.1967T>C (p.I656T) alteration is located in exon 12 (coding exon 12) of the CRNKL1 gene. This alteration results from a T to C substitution at nucleotide position 1967, causing the isoleucine (I) at amino acid position 656 to be replaced by a threonine (T). 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