chr17-61680181-TA-T

Position:

• chr17-61680181-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_032043.3(BRIP1):​c.*3114delT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.39 (9122 hom., cov: 0)
• Consequence: BRIP1 NM_032043.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 0.615

Genes affected

BRIP1 (HGNC:20473): (BRCA1 interacting helicase 1) The protein encoded by this gene is a member of the RecQ DEAH helicase family and interacts with the BRCT repeats of breast cancer, type 1 (BRCA1). The bound complex is important in the normal double-strand break repair function of breast cancer, type 1 (BRCA1). This gene may be a target of germline cancer-inducing mutations. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-61680181-TA-T is Benign according to our data. Variant chr17-61680181-TA-T is described in ClinVar as [Likely_benign]. Clinvar id is 324300.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRIP1	NM_032043.3	c.*3114delT		3_prime_UTR_variant	20/20	ENST00000259008.7	NP_114432.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRIP1	ENST00000259008	c.*3114delT		3_prime_UTR_variant	20/20	1	NM_032043.3	ENSP00000259008.2
BRIP1	ENST00000682755	c.*3114delT		3_prime_UTR_variant	18/18			ENSP00000507660.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 49269 AN: 127916 Hom.: 9119 Cov.: 0

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.385 AC: 49285 AN: 127912 Hom.: 9122 Cov.: 0 AF XY: 0.380 AC XY: 23141 AN XY: 60872

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.260

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.380

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

Fanconi anemia Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Breast neoplasm Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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: rs35235448; hg19: chr17-59757542;