5-81207321-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_006909.3(RASGRF2):c.3043C>T(p.His1015Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006909.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RASGRF2 | NM_006909.3 | c.3043C>T | p.His1015Tyr | missense_variant | Exon 21 of 27 | ENST00000265080.9 | NP_008840.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RASGRF2 | ENST00000265080.9 | c.3043C>T | p.His1015Tyr | missense_variant | Exon 21 of 27 | 1 | NM_006909.3 | ENSP00000265080.4 | ||
RASGRF2 | ENST00000503795.1 | n.3043C>T | non_coding_transcript_exon_variant | Exon 21 of 28 | 1 | ENSP00000421771.1 | ||||
CKMT2-AS1 | ENST00000503483.6 | n.333-2998G>A | intron_variant | Intron 2 of 2 | 3 | |||||
CKMT2-AS1 | ENST00000663674.1 | n.187-3794G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461836Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727222
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3043C>T (p.H1015Y) alteration is located in exon 1 (coding exon 1) of the RASGRF2 gene. This alteration results from a C to T substitution at nucleotide position 3043, causing the histidine (H) at amino acid position 1015 to be replaced by a tyrosine (Y). 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