chr4-56307569-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.155G>A(p.Arg52Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,614,096 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.155G>A | p.Arg52Gln | missense_variant | 5/11 | ENST00000682029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACD | ENST00000682029.1 | c.155G>A | p.Arg52Gln | missense_variant | 5/11 | NM_001393381.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000204 AC: 31AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000220 AC: 55AN: 249486Hom.: 0 AF XY: 0.000222 AC XY: 30AN XY: 135344
GnomAD4 exome AF: 0.000209 AC: 306AN: 1461850Hom.: 0 Cov.: 31 AF XY: 0.000212 AC XY: 154AN XY: 727216
GnomAD4 genome ? AF: 0.000204 AC: 31AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 21, 2022 | The c.155G>A (p.R52Q) alteration is located in exon 5 (coding exon 2) of the KIAA1211 gene. This alteration results from a G to A substitution at nucleotide position 155, causing the arginine (R) at amino acid position 52 to be replaced by a glutamine (Q). 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