2-33539176-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001139488.2(RASGRP3):c.1244C>A(p.Thr415Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000036 in 1,609,828 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.1244C>A | p.Thr415Lys | missense_variant | 12/18 | ENST00000403687.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGRP3 | ENST00000403687.8 | c.1244C>A | p.Thr415Lys | missense_variant | 12/18 | 1 | NM_001139488.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 151970Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000289 AC: 7AN: 242318Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131200
GnomAD4 exome AF: 0.0000357 AC: 52AN: 1457858Hom.: 0 Cov.: 31 AF XY: 0.0000469 AC XY: 34AN XY: 724760
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 151970Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74194
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 04, 2022 | The c.1244C>A (p.T415K) alteration is located in exon 12 (coding exon 10) of the RASGRP3 gene. This alteration results from a C to A substitution at nucleotide position 1244, causing the threonine (T) at amino acid position 415 to be replaced by a lysine (K). 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