13-32315355-ATGCCTGACAAGGAATTTCCTTTCGCCACACTGAGAAATACCCGCAGCGGCCCACCCAGGCCTGACTTCCGGGTGGTGCGTGTGCTGCGTGTCGCGTCACGGCGTCACGTGGCCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGGTTAGTGGTGGTGGTAGTGGGTTGGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGGCGGGGGAGCGCCTCACGCCCCGGGTCGCTGCCGCGGCTTCTTGCCCTTTTGTCTCTGCCAACCCCCACCCATGCCTGAGAGAAAGGTCCTTGCCCGAAGGCAGATTTTCGCCAAGCAAATTCGAGCCCCGCCCCTTCCCTGGGTCTCCATTTCCCGCCTCCGGCCCGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGC-A

Position:

• chr13-32315355-ATGCCTGACAAGGAATTTCCTTTCGCCACACTGAGAAATACCCGCAGCGGCCCACCCAGGCCTGACTTCCGGGTGGTGCGTGTGCTGCGTGTCGCGTCACGGCGTCACGTGGCCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGGTTAGTGGTGGTGGTAGTGGGTTGGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGGCGGGGGAGCGCCTCACGCCCCGGGTCGCTGCCGCGGCTTCTTGCCCTTTTGTCTCTGCCAACCCCCACCCATGCCTGAGAGAAAGGTCCTTGCCCGAAGGCAGATTTTCGCCAAGCAAATTCGAGCCCCGCCCCTTCCCTGGGTCTCCATTTCCCGCCTCCGGCCCGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGC-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The 13-32315355-ATGCCTGACAAGGAATTTCCTTTCGCCACACTGAGAAATACCCGCAGCGGCCCACCCAGGCCTGACTTCCGGGTGGTGCGTGTGCTGCGTGTCGCGTCACGGCGTCACGTGGCCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGGTTAGTGGTGGTGGTAGTGGGTTGGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGGCGGGGGAGCGCCTCACGCCCCGGGTCGCTGCCGCGGCTTCTTGCCCTTTTGTCTCTGCCAACCCCCACCCATGCCTGAGAGAAAGGTCCTTGCCCGAAGGCAGATTTTCGCCAAGCAAATTCGAGCCCCGCCCCTTCCCTGGGTCTCCATTTCCCGCCTCCGGCCCGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGC-A variant causes a splice donor, splice donor 5th base, 5 prime UTR, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: BRCA2 NM_000059.4 splice_donor, splice_donor_5th_base, 5_prime_UTR, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: -0.00500

Genes affected

ZAR1L (HGNC:37116): (zygote arrest 1 like) This gene encodes a member of the ZAR1 family that is predominantly expressed in oocytes and early embryos. The protein may function as an RNA regulator in early embryos. [provided by RefSeq, Apr 2010]

BRCA2 (HGNC:1101): (BRCA2 DNA repair associated) Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The largest exon in both genes is exon 11, which harbors the most important and frequent mutations in breast cancer patients. The BRCA2 gene was found on chromosome 13q12.3 in human. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease,
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 13-32315355-ATGCCTGACAAGGAATTTCCTTTCGCCACACTGAGAAATACCCGCAGCGGCCCACCCAGGCCTGACTTCCGGGTGGTGCGTGTGCTGCGTGTCGCGTCACGGCGTCACGTGGCCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGGTTAGTGGTGGTGGTAGTGGGTTGGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGGCGGGGGAGCGCCTCACGCCCCGGGTCGCTGCCGCGGCTTCTTGCCCTTTTGTCTCTGCCAACCCCCACCCATGCCTGAGAGAAAGGTCCTTGCCCGAAGGCAGATTTTCGCCAAGCAAATTCGAGCCCCGCCCCTTCCCTGGGTCTCCATTTCCCGCCTCCGGCCCGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGC-A is Pathogenic according to our data. Variant chr13-32315355-ATGCCTGACAAGGAATTTCCTTTCGCCACACTGAGAAATACCCGCAGCGGCCCACCCAGGCCTGACTTCCGGGTGGTGCGTGTGCTGCGTGTCGCGTCACGGCGTCACGTGGCCAGCGCGGGCTTGTGGCGCGAGCTTCTGAAACTAGGCGGCAGAGGCGGAGCCGCTGTGGCACTGCTGCGCCTCTGCTGCGCCTCGGGTGTCTTTTGCGGCGGTGGGTCGCCGCCGGGAGAAGCGTGAGGGGACAGATTTGTGACCGGCGCGGTTTTTGTCAGCTTACTCCGGCCAAAAAAGAACTGCACCTCTGGAGCGGGTTAGTGGTGGTGGTAGTGGGTTGGGACGAGCGCGTCTTCCGCAGTCCCAGTCCAGCGTGGCGGGGGAGCGCCTCACGCCCCGGGTCGCTGCCGCGGCTTCTTGCCCTTTTGTCTCTGCCAACCCCCACCCATGCCTGAGAGAAAGGTCCTTGCCCGAAGGCAGATTTTCGCCAAGCAAATTCGAGCCCCGCCCCTTCCCTGGGTCTCCATTTCCCGCCTCCGGCCCGGCCTTTGGGCTCCGCCTTCAGCTCAAGACTTAACTTCCCTCCCAGCTGTCCCAGATGACGCCATCTGAAATTTCTTGGAAACACGATCACTTTAACGGAATATTGCTGTTTTGGGGAAGTGTTTTACAGCTGCTGGGCACGCTGTATTTGCCTTACTTAAGCCCCTGGTAATTGCTGTATTCCGAAGACATGCTGATGGGAATTACCAGGCGGCGTTGGTCTCTAACTGGAGCCCTCTGTCCCCACTAGCCACGCGTCACTGGTTAGCGTGATTGAAACTAAATCGTATGAAAATCCTCTTCTCTAGTCGCACTAGCCACGTTTCGAGTGCTTAATGTGGCTAGTGGCACCGGTTTGGACAGCACAGCTGTAAAATGTTCCCATCCTCACAGTAAGC-A is described in ClinVar as [Pathogenic]. Clinvar id is 873424.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZAR1L	NM_001136571.2			5_prime_UTR_variant	1/6	ENST00000533490.7	NP_001130043.1
BRCA2	NM_000059.4			splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant	1/27	ENST00000380152.8	NP_000050.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZAR1L	ENST00000533490.7			5_prime_UTR_variant	1/6	5	NM_001136571.2	ENSP00000437289	P1
BRCA2	ENST00000380152.8			splice_donor_variant, splice_donor_5th_base_variant, 5_prime_UTR_variant, intron_variant	1/27	5	NM_000059.4	ENSP00000369497	A2

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hereditary breast ovarian cancer syndrome;C2675520:Breast-ovarian cancer, familial, susceptibility to, 2 Pathogenic:1

Pathogenic, no assertion criteria provided

research

King Laboratory, University of Washington

Sep 01, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2072242904; hg19: chr13-32889492;