12-3615390-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001144958.2(CRACR2A):c.2161G>A(p.Gly721Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000419 in 1,551,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/19 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRACR2A | NM_001144958.2 | c.2161G>A | p.Gly721Ser | missense_variant | 20/20 | ENST00000440314.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRACR2A | ENST00000440314.7 | c.2161G>A | p.Gly721Ser | missense_variant | 20/20 | 2 | NM_001144958.2 | P1 | |
CRACR2A | ENST00000333750.9 | c.*1158G>A | 3_prime_UTR_variant, NMD_transcript_variant | 14/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000520 AC: 8AN: 153816Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81596
GnomAD4 exome AF: 0.0000336 AC: 47AN: 1399288Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 19AN XY: 690154
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152152Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.2161G>A (p.G721S) alteration is located in exon 20 (coding exon 17) of the CRACR2A gene. This alteration results from a G to A substitution at nucleotide position 2161, causing the glycine (G) at amino acid position 721 to be replaced by a serine (S). 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