Variant chr17-61780448-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032043.3(BRIP1):c.1795-47G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 1,550,092 control chromosomes in the GnomAD database, including 438,318 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.78 ( 46475 hom., cov: 31)

Exomes 𝑓: 0.75 ( 391843 hom. )

Consequence

BRIP1
NM_032043.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.152

Variant links:

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]

BRIP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 17-61780448-C-G is Benign according to our data. Variant chr17-61780448-C-G is described in ClinVar as [Benign]. Clinvar id is 262005.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr17-61780448-C-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRIP1	NM_032043.3 linkuse as main transcript	c.1795-47G>C		intron_variant		ENST00000259008.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRIP1	ENST00000259008.7 linkuse as main transcript	c.1795-47G>C		intron_variant		1	NM_032043.3	P2	Q9BX63-1

Frequencies

GnomAD3 genomes

AF:

0.778

AC:

118178

AN:

151952

Hom.:

46452

Cov.:

show subpopulations

Gnomad AFR

AF:

0.854

Gnomad AMI

AF:

0.879

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.720

Gnomad EAS

AF:

0.820

Gnomad SAS

AF:

0.797

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.756

Gnomad OTH

AF:

0.763

GnomAD3 exomes

AF:

0.737

AC:

182419

AN:

247544

Hom.:

68670

AF XY:

0.746

AC XY:

100390

AN XY:

134634

show subpopulations

Gnomad AFR exome

AF:

0.856

Gnomad AMR exome

AF:

0.496

Gnomad ASJ exome

AF:

0.744

Gnomad EAS exome

AF:

0.829

Gnomad SAS exome

AF:

0.793

Gnomad FIN exome

AF:

0.804

Gnomad NFE exome

AF:

0.751

Gnomad OTH exome

AF:

0.738

GnomAD4 exome

AF:

0.746

AC:

1043578

AN:

1398022

Hom.:

391843

Cov.:

AF XY:

0.749

AC XY:

523283

AN XY:

698728

show subpopulations

Gnomad4 AFR exome

AF:

0.861

Gnomad4 AMR exome

AF:

0.511

Gnomad4 ASJ exome

AF:

0.746

Gnomad4 EAS exome

AF:

0.787

Gnomad4 SAS exome

AF:

0.794

Gnomad4 FIN exome

AF:

0.801

Gnomad4 NFE exome

AF:

0.744

Gnomad4 OTH exome

AF:

0.761

GnomAD4 genome

AF:

0.778

AC:

118246

AN:

152070

Hom.:

46475

Cov.:

AF XY:

0.777

AC XY:

57771

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.853

Gnomad4 AMR

AF:

0.632

Gnomad4 ASJ

AF:

0.720

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.795

Gnomad4 FIN

AF:

0.810

Gnomad4 NFE

AF:

0.756

Gnomad4 OTH

AF:

0.765

Alfa

AF:

0.764

Hom.:

7904

Bravo

AF:

0.764

Asia WGS

AF:

0.803

AC:

2793

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.9

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over