chr2-33558277-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001139488.2(RASGRP3):c.1646G>A(p.Arg549Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000233 in 1,613,264 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_001139488.2 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 |
---|---|---|---|---|---|---|---|
RASGRP3 | NM_001139488.2 | c.1646G>A | p.Arg549Gln | missense_variant | 16/18 | ENST00000403687.8 | |
RASGRP3-AS1 | NR_146505.1 | n.2497-2963C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGRP3 | ENST00000403687.8 | c.1646G>A | p.Arg549Gln | missense_variant | 16/18 | 1 | NM_001139488.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.000118 AC: 18AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000726 AC: 18AN: 248040Hom.: 0 AF XY: 0.0000743 AC XY: 10AN XY: 134604
GnomAD4 exome AF: 0.000245 AC: 358AN: 1461212Hom.: 0 Cov.: 31 AF XY: 0.000239 AC XY: 174AN XY: 726828
GnomAD4 genome ? AF: 0.000118 AC: 18AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.1646G>A (p.R549Q) alteration is located in exon 16 (coding exon 14) of the RASGRP3 gene. This alteration results from a G to A substitution at nucleotide position 1646, causing the arginine (R) at amino acid position 549 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