7-140924774-GGGAGGCGGAGGCGGAGGC-GGGAGGC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_004333.6(BRAF):​c.-83_-72delGCCTCCGCCTCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000985 in 586,848 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00047 ( 1 hom. )

Consequence

BRAF
NM_004333.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
Variant links:
Genes affected
BRAF (HGNC:1097): (B-Raf proto-oncogene, serine/threonine kinase) This gene encodes a protein belonging to the RAF family of serine/threonine protein kinases. This protein plays a role in regulating the MAP kinase/ERK signaling pathway, which affects cell division, differentiation, and secretion. Mutations in this gene, most commonly the V600E mutation, are the most frequently identified cancer-causing mutations in melanoma, and have been identified in various other cancers as well, including non-Hodgkin lymphoma, colorectal cancer, thyroid carcinoma, non-small cell lung carcinoma, hairy cell leukemia and adenocarcinoma of lung. Mutations in this gene are also associated with cardiofaciocutaneous, Noonan, and Costello syndromes, which exhibit overlapping phenotypes. A pseudogene of this gene has been identified on the X chromosome. [provided by RefSeq, Aug 2017]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00249 (374/150376) while in subpopulation AFR AF= 0.00704 (289/41074). AF 95% confidence interval is 0.00637. There are 0 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
High AC in GnomAd4 at 374 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BRAFNM_001374258.1 linkc.-83_-72delGCCTCCGCCTCC 5_prime_UTR_variant Exon 1 of 20 ENST00000644969.2 NP_001361187.1
BRAFNM_004333.6 linkc.-83_-72delGCCTCCGCCTCC 5_prime_UTR_variant Exon 1 of 18 ENST00000646891.2 NP_004324.2 P15056

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BRAFENST00000644969.2 linkc.-83_-72delGCCTCCGCCTCC 5_prime_UTR_variant Exon 1 of 20 NM_001374258.1 ENSP00000496776.1 A0A2R8Y8E0
BRAFENST00000646891.2 linkc.-83_-72delGCCTCCGCCTCC 5_prime_UTR_variant Exon 1 of 18 NM_004333.6 ENSP00000493543.1 P15056

Frequencies

GnomAD3 genomes
AF:
0.00248
AC:
373
AN:
150270
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.00706
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00225
Gnomad ASJ
AF:
0.00347
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000417
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000475
Gnomad OTH
AF:
0.00194
GnomAD4 exome
AF:
0.000467
AC:
204
AN:
436472
Hom.:
1
AF XY:
0.000442
AC XY:
105
AN XY:
237424
show subpopulations
Gnomad4 AFR exome
AF:
0.00470
Gnomad4 AMR exome
AF:
0.000715
Gnomad4 ASJ exome
AF:
0.00145
Gnomad4 EAS exome
AF:
0.000127
Gnomad4 SAS exome
AF:
0.000134
Gnomad4 FIN exome
AF:
0.000101
Gnomad4 NFE exome
AF:
0.000310
Gnomad4 OTH exome
AF:
0.00108
GnomAD4 genome
AF:
0.00249
AC:
374
AN:
150376
Hom.:
0
Cov.:
30
AF XY:
0.00245
AC XY:
180
AN XY:
73504
show subpopulations
Gnomad4 AFR
AF:
0.00704
Gnomad4 AMR
AF:
0.00225
Gnomad4 ASJ
AF:
0.00347
Gnomad4 EAS
AF:
0.000197
Gnomad4 SAS
AF:
0.000418
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000475
Gnomad4 OTH
AF:
0.00192
Alfa
AF:
0.0000543
Hom.:
0
Bravo
AF:
0.00284

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs727502907; hg19: chr7-140624574; API