3-12583765-CTGTT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_002880.4(RAF1):​c.*745_*748delAACA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 233,406 control chromosomes in the GnomAD database, including 693 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.069 ( 436 hom., cov: 31)
Exomes 𝑓: 0.075 ( 257 hom. )

Consequence

RAF1
NM_002880.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:3

Conservation

PhyloP100: 0.730
Variant links:
Genes affected
RAF1 (HGNC:9829): (Raf-1 proto-oncogene, serine/threonine kinase) This gene is the cellular homolog of viral raf gene (v-raf). The encoded protein is a MAP kinase kinase kinase (MAP3K), which functions downstream of the Ras family of membrane associated GTPases to which it binds directly. Once activated, the cellular RAF1 protein can phosphorylate to activate the dual specificity protein kinases MEK1 and MEK2, which in turn phosphorylate to activate the serine/threonine specific protein kinases, ERK1 and ERK2. Activated ERKs are pleiotropic effectors of cell physiology and play an important role in the control of gene expression involved in the cell division cycle, apoptosis, cell differentiation and cell migration. Mutations in this gene are associated with Noonan syndrome 5 and LEOPARD syndrome 2. [provided by RefSeq, Jul 2008]
MKRN2 (HGNC:7113): (makorin ring finger protein 2) This gene encodes a probable E3 ubiquitin ligase containing several zinc finger domains, that is a member of the makorin RING zinc-finger protein family. This gene overlaps the v-raf-1 murine leukemia viral oncogene homolog 1 (RAF1) gene in an antisense orientation and may have a co-regulatory function with RAF1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0949 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RAF1NM_002880.4 linkc.*745_*748delAACA 3_prime_UTR_variant Exon 17 of 17 ENST00000251849.9 NP_002871.1 P04049-1L7RRS6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RAF1ENST00000251849 linkc.*745_*748delAACA 3_prime_UTR_variant Exon 17 of 17 1 NM_002880.4 ENSP00000251849.4 P04049-1

Frequencies

GnomAD3 genomes
AF:
0.0693
AC:
10529
AN:
152006
Hom.:
437
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0330
Gnomad AMI
AF:
0.135
Gnomad AMR
AF:
0.0576
Gnomad ASJ
AF:
0.105
Gnomad EAS
AF:
0.00212
Gnomad SAS
AF:
0.0263
Gnomad FIN
AF:
0.0855
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.0969
Gnomad OTH
AF:
0.0707
GnomAD4 exome
AF:
0.0751
AC:
6104
AN:
81278
Hom.:
257
AF XY:
0.0760
AC XY:
2843
AN XY:
37418
show subpopulations
Gnomad4 AFR exome
AF:
0.0289
Gnomad4 AMR exome
AF:
0.0469
Gnomad4 ASJ exome
AF:
0.101
Gnomad4 EAS exome
AF:
0.00132
Gnomad4 SAS exome
AF:
0.0227
Gnomad4 FIN exome
AF:
0.112
Gnomad4 NFE exome
AF:
0.0937
Gnomad4 OTH exome
AF:
0.0830
GnomAD4 genome
AF:
0.0692
AC:
10527
AN:
152128
Hom.:
436
Cov.:
31
AF XY:
0.0664
AC XY:
4942
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.0330
Gnomad4 AMR
AF:
0.0576
Gnomad4 ASJ
AF:
0.105
Gnomad4 EAS
AF:
0.00212
Gnomad4 SAS
AF:
0.0263
Gnomad4 FIN
AF:
0.0855
Gnomad4 NFE
AF:
0.0968
Gnomad4 OTH
AF:
0.0691
Bravo
AF:
0.0655

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Noonan syndrome with multiple lentigines Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Uncertain:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Noonan syndrome Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs371820097; hg19: chr3-12625264; API