chr4-56314308-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001393381.1(CRACD):c.806T>G(p.Leu269Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000828 in 1,552,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L269I) has been classified as Likely benign.
Frequency
Consequence
NM_001393381.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRACD | NM_001393381.1 | c.806T>G | p.Leu269Arg | missense_variant | 8/11 | ENST00000682029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACD | ENST00000682029.1 | c.806T>G | p.Leu269Arg | missense_variant | 8/11 | NM_001393381.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000878 AC: 133AN: 151480Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00111 AC: 172AN: 155244Hom.: 0 AF XY: 0.000970 AC XY: 80AN XY: 82460
GnomAD4 exome AF: 0.000822 AC: 1152AN: 1400836Hom.: 0 Cov.: 67 AF XY: 0.000819 AC XY: 566AN XY: 691124
GnomAD4 genome ? AF: 0.000877 AC: 133AN: 151598Hom.: 0 Cov.: 33 AF XY: 0.000864 AC XY: 64AN XY: 74080
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 27, 2022 | The c.806T>G (p.L269R) alteration is located in exon 8 (coding exon 5) of the KIAA1211 gene. This alteration results from a T to G substitution at nucleotide position 806, causing the leucine (L) at amino acid position 269 to be replaced by an arginine (R). 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