chr17-61684345-A-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.34

Publications

12 publications found
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 Gene-Disease associations (from GenCC):
  • familial ovarian cancer
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • Fanconi anemia
    Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
  • Fanconi anemia complementation group J
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • hereditary breast carcinoma
    Inheritance: AD Classification: STRONG, LIMITED, NO_KNOWN Submitted by: ClinGen, Genomics England PanelApp, Ambry Genetics, Labcorp Genetics (formerly Invitae)
  • colorectal adenoma
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank MANE Protein UniProt
BRIP1NM_032043.3 linkc.2906-205T>C intron_variant Intron 19 of 19 ENST00000259008.7 NP_114432.2 Q9BX63-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BRIP1ENST00000259008.7 linkc.2906-205T>C intron_variant Intron 19 of 19 1 NM_032043.3 ENSP00000259008.2 Q9BX63-1

Frequencies

GnomAD3 genomes
AF:
0.338
AC:
51382
AN:
151846
Hom.:
8904
Cov.:
31
show subpopulations
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
show subpopulations
African (AFR)
AF:
0.353
AC:
14621
AN:
41442
American (AMR)
AF:
0.298
AC:
4546
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.322
AC:
1116
AN:
3468
East Asian (EAS)
AF:
0.490
AC:
2531
AN:
5162
South Asian (SAS)
AF:
0.263
AC:
1267
AN:
4818
European-Finnish (FIN)
AF:
0.243
AC:
2569
AN:
10576
Middle Eastern (MID)
AF:
0.473
AC:
139
AN:
294
European-Non Finnish (NFE)
AF:
0.348
AC:
23637
AN:
67932
Other (OTH)
AF:
0.358
AC:
754
AN:
2104
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1728
3457
5185
6914
8642
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
506
1012
1518
2024
2530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.346
Hom.:
25698
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
LINK: link

Submissions by phenotype

not provided Benign:1
Jun 22, 2018
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.58
CADD
Benign
10
DANN
Benign
0.94
PhyloP100
1.3
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs11871785; hg19: chr17-59761706; API