chr4-56314296-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001393381.1(CRACD):c.794G>A(p.Arg265Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000971 in 1,555,214 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 (★).
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.794G>A | p.Arg265Lys | missense_variant | 8/11 | ENST00000682029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACD | ENST00000682029.1 | c.794G>A | p.Arg265Lys | missense_variant | 8/11 | NM_001393381.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000191 AC: 3AN: 157200Hom.: 0 AF XY: 0.0000120 AC XY: 1AN XY: 83350
GnomAD4 exome AF: 0.000100 AC: 141AN: 1403044Hom.: 0 Cov.: 30 AF XY: 0.0000910 AC XY: 63AN XY: 692328
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.794G>A (p.R265K) alteration is located in exon 8 (coding exon 5) of the KIAA1211 gene. This alteration results from a G to A substitution at nucleotide position 794, causing the arginine (R) at amino acid position 265 to be replaced by a lysine (K). 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