chr12-3627694-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144958.2(CRACR2A):c.1748G>A(p.Arg583His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000171 in 1,551,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144958.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRACR2A | NM_001144958.2 | c.1748G>A | p.Arg583His | missense_variant | 16/20 | ENST00000440314.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACR2A | ENST00000440314.7 | c.1748G>A | p.Arg583His | missense_variant | 16/20 | 2 | NM_001144958.2 | P1 | |
CRACR2A | ENST00000333750.9 | c.*745G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000158 AC: 24AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000575 AC: 9AN: 156658Hom.: 0 AF XY: 0.0000361 AC XY: 3AN XY: 82988
GnomAD4 exome AF: 0.000172 AC: 241AN: 1399462Hom.: 0 Cov.: 36 AF XY: 0.000180 AC XY: 124AN XY: 690244
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.1748G>A (p.R583H) alteration is located in exon 16 (coding exon 13) of the CRACR2A gene. This alteration results from a G to A substitution at nucleotide position 1748, causing the arginine (R) at amino acid position 583 to be replaced by a histidine (H). 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