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
NM_004333.6 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00
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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAF | ENST00000644969.2 | c.-83_-72delGCCTCCGCCTCC | 5_prime_UTR_variant | Exon 1 of 20 | NM_001374258.1 | ENSP00000496776.1 | ||||
BRAF | ENST00000646891.2 | c.-83_-72delGCCTCCGCCTCC | 5_prime_UTR_variant | Exon 1 of 18 | NM_004333.6 | ENSP00000493543.1 |
Frequencies
GnomAD3 genomes AF: 0.00248 AC: 373AN: 150270Hom.: 0 Cov.: 30
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GnomAD4 exome AF: 0.000467 AC: 204AN: 436472Hom.: 1 AF XY: 0.000442 AC XY: 105AN XY: 237424
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GnomAD4 genome AF: 0.00249 AC: 374AN: 150376Hom.: 0 Cov.: 30 AF XY: 0.00245 AC XY: 180AN XY: 73504
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at