chr4-56307673-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001393381.1(CRACD):c.259A>G(p.Ile87Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000582 in 1,614,196 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.259A>G | p.Ile87Val | missense_variant | 5/11 | ENST00000682029.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACD | ENST00000682029.1 | c.259A>G | p.Ile87Val | missense_variant | 5/11 | NM_001393381.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000721 AC: 18AN: 249504Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135370
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727228
GnomAD4 genome ? AF: 0.000236 AC: 36AN: 152360Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 26, 2022 | The c.259A>G (p.I87V) alteration is located in exon 5 (coding exon 2) of the KIAA1211 gene. This alteration results from a A to G substitution at nucleotide position 259, causing the isoleucine (I) at amino acid position 87 to be replaced by a valine (V). 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