rs5746220
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
This summary comes from the ClinGen Evidence Repository: The filtering allele frequency of the c.923C>T (p.Pro308Leu) variant in the RAF1 gene is 1.516% (179/10394) of African chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581) LINK:https://erepo.genome.network/evrepo/ui/classification/CA134762/MONDO:0021060/004
Frequency
Consequence
NM_002880.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00521 AC: 793AN: 152112Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00132 AC: 332AN: 251370Hom.: 1 AF XY: 0.00100 AC XY: 136AN XY: 135884
GnomAD4 exome AF: 0.000538 AC: 787AN: 1461888Hom.: 15 Cov.: 32 AF XY: 0.000479 AC XY: 348AN XY: 727246
GnomAD4 genome AF: 0.00520 AC: 792AN: 152230Hom.: 6 Cov.: 33 AF XY: 0.00511 AC XY: 380AN XY: 74414
ClinVar
Submissions by phenotype
not specified Benign:4
Pro308Leu in exon 9 of RAF1: This variant is not expected to have clinical signi ficance because it has been identified in 1.4% (54/3738) of African American chr omosomes from a broad population by the NHLBI Exome Sequencing Project (http://e vs.gs.washington.edu/EVS/; dbSNP rs5746220). -
- -
- -
- -
not provided Benign:4
- -
- -
- -
- -
RASopathy Benign:2
The filtering allele frequency of the c.923C>T (p.Pro308Leu) variant in the RAF1 gene is 1.516% (179/10394) of African chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581) -
- -
LEOPARD syndrome 2 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Noonan syndrome 5 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Noonan syndrome and Noonan-related syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at