rs11871785

chr17-61684345-A-Gchr17-61684345-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_032043.3(BRIP1):c.2906-205T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,964 control chromosomes in the GnomAD database, including 8,912 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (8912 hom., cov: 31)
• Consequence: BRIP1 NM_032043.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.34

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BP6: Variant 17-61684345-A-G is Benign according to our data. Variant chr17-61684345-A-G is described in ClinVar as [Benign]. Clinvar id is 1237030.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRIP1	NM_032043.3	c.2906-205T>C		intron_variant		ENST00000259008.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRIP1	ENST00000259008.7	c.2906-205T>C		intron_variant		1	NM_032043.3	P2

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51382 AN: 151846 Hom.: 8904 Cov.: 31

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.338 AC: 51431 AN: 151964 Hom.: 8912 Cov.: 31 AF XY: 0.333 AC XY: 24721 AN XY: 74264

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.358

Alfa AF: 0.347 Hom.: 14471

Bravo AF: 0.344

Asia WGS AF: 0.334 AC: 1162 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
Cadd	Benign	10
Dann	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11871785; hg19: chr17-59761706;