chr15-79003846-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001145648.3(RASGRF1):c.2405C>T(p.Thr802Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000609 in 1,612,894 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001145648.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASGRF1 | NM_001145648.3 | c.2405C>T | p.Thr802Met | missense_variant | 15/27 | ENST00000558480.7 | |
LOC105370917 | XR_932518.3 | n.348-2001G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASGRF1 | ENST00000558480.7 | c.2405C>T | p.Thr802Met | missense_variant | 15/27 | 2 | NM_001145648.3 | P1 | |
RASGRF1 | ENST00000394745.3 | c.101C>T | p.Thr34Met | missense_variant | 2/14 | 1 | |||
RASGRF1 | ENST00000560334.5 | n.2275C>T | non_coding_transcript_exon_variant | 14/24 | 1 | ||||
RASGRF1 | ENST00000419573.7 | c.2453C>T | p.Thr818Met | missense_variant | 16/28 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00311 AC: 473AN: 152202Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.000912 AC: 228AN: 250040Hom.: 1 AF XY: 0.000629 AC XY: 85AN XY: 135184
GnomAD4 exome AF: 0.000348 AC: 509AN: 1460574Hom.: 2 Cov.: 33 AF XY: 0.000289 AC XY: 210AN XY: 726534
GnomAD4 genome AF: 0.00311 AC: 473AN: 152320Hom.: 4 Cov.: 32 AF XY: 0.00306 AC XY: 228AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at