rs196432
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000412742.5(RCAN3):c.491G>A(p.Arg164Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.476 in 1,588,326 control chromosomes in the GnomAD database, including 182,348 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000412742.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RCAN3 | NM_013441.4 | c.663G>A | p.Thr221= | synonymous_variant | 5/5 | ENST00000374395.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RCAN3 | ENST00000374395.9 | c.663G>A | p.Thr221= | synonymous_variant | 5/5 | 1 | NM_013441.4 | P1 | |
RCAN3AS | ENST00000651630.1 | n.142+45C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.465 AC: 70702AN: 151946Hom.: 16755 Cov.: 33
GnomAD3 exomes AF: 0.472 AC: 106249AN: 225008Hom.: 25790 AF XY: 0.472 AC XY: 58052AN XY: 123048
GnomAD4 exome AF: 0.477 AC: 684694AN: 1436262Hom.: 165584 Cov.: 55 AF XY: 0.475 AC XY: 339842AN XY: 714754
GnomAD4 genome ? AF: 0.465 AC: 70735AN: 152064Hom.: 16764 Cov.: 33 AF XY: 0.464 AC XY: 34510AN XY: 74326
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at