17-43104083-AAAGAAGAAG-AAAG

Variant names:

• chr17-43104083-AAAGAAG-A
• rs147856441
• NM_007294.4:c.441+33_441+38delCTTCTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_007294.4(BRCA1):​c.441+33_441+38delCTTCTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,124,644 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00017 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000069 (0 hom.)
• Consequence: BRCA1 NM_007294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 6 publications found

Genes affected

BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]

BRCA1 Gene-Disease associations (from GenCC):

• breast-ovarian cancer, familial, susceptibility to, 1

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• Fanconi anemia, complementation group S

  Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• pancreatic cancer, susceptibility to, 4

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• hereditary breast ovarian cancer syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRCA1	NM_007294.4	c.441+33_441+38delCTTCTT		intron_variant	Intron 6 of 22	ENST00000357654.9	NP_009225.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRCA1	ENST00000357654.9	c.441+33_441+38delCTTCTT		intron_variant	Intron 6 of 22	1	NM_007294.4	ENSP00000350283.3

Frequencies

GnomAD3 genomes AF: 0.000166 AC: 12 AN: 72152 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000815

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000145

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000483

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000261

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000313 AC: 6 AN: 191546 AF XY: 0.0000194

Gnomad AFR exome AF: 0.0000731

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000706

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000448

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000694 AC: 73 AN: 1052492 Hom.: 0 AF XY: 0.0000673 AC XY: 34 AN XY: 505098

African (AFR) AF: 0.000122 AC: 3 AN: 24564

American (AMR) AF: 0.00 AC: 0 AN: 19026

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12856

East Asian (EAS) AF: 0.00 AC: 0 AN: 18230

South Asian (SAS) AF: 0.0000307 AC: 1 AN: 32522

European-Finnish (FIN) AF: 0.0000532 AC: 1 AN: 18792

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3170

European-Non Finnish (NFE) AF: 0.0000759 AC: 67 AN: 883244

Other (OTH) AF: 0.0000249 AC: 1 AN: 40088

GnomAD4 genome AF: 0.000166 AC: 12 AN: 72152 Hom.: 0 Cov.: 0 AF XY: 0.000174 AC XY: 6 AN XY: 34568

African (AFR) AF: 0.0000815 AC: 2 AN: 24542

American (AMR) AF: 0.000145 AC: 1 AN: 6916

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1398

East Asian (EAS) AF: 0.000483 AC: 1 AN: 2070

South Asian (SAS) AF: 0.00 AC: 0 AN: 1318

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3742

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 130

European-Non Finnish (NFE) AF: 0.000261 AC: 8 AN: 30636

Other (OTH) AF: 0.00 AC: 0 AN: 928

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.70
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs147856441; hg19: chr17-41256100;