17-61680480-C-CTTTCTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_032043.3(BRIP1):​c.*2815_*2816insAAAAGAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.012 ( 46 hom., cov: 0)

Consequence

BRIP1
NM_032043.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0550
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0122 (1517/124002) while in subpopulation SAS AF= 0.0322 (127/3942). AF 95% confidence interval is 0.0277. There are 46 homozygotes in gnomad4. There are 731 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 46 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BRIP1NM_032043.3 linkc.*2815_*2816insAAAAGAAA 3_prime_UTR_variant 20/20 ENST00000259008.7 NP_114432.2 Q9BX63-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BRIP1ENST00000259008 linkc.*2815_*2816insAAAAGAAA 3_prime_UTR_variant 20/201 NM_032043.3 ENSP00000259008.2 Q9BX63-1
BRIP1ENST00000682755 linkc.*2815_*2816insAAAAGAAA 3_prime_UTR_variant 18/18 ENSP00000507660.1 A0A804HJV4

Frequencies

GnomAD3 genomes
AF:
0.0123
AC:
1521
AN:
124026
Hom.:
47
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.00363
Gnomad AMI
AF:
0.0500
Gnomad AMR
AF:
0.00906
Gnomad ASJ
AF:
0.0136
Gnomad EAS
AF:
0.0137
Gnomad SAS
AF:
0.0325
Gnomad FIN
AF:
0.00991
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0157
Gnomad OTH
AF:
0.00800
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0122
AC:
1517
AN:
124002
Hom.:
46
Cov.:
0
AF XY:
0.0125
AC XY:
731
AN XY:
58524
show subpopulations
Gnomad4 AFR
AF:
0.00363
Gnomad4 AMR
AF:
0.00906
Gnomad4 ASJ
AF:
0.0136
Gnomad4 EAS
AF:
0.0138
Gnomad4 SAS
AF:
0.0322
Gnomad4 FIN
AF:
0.00991
Gnomad4 NFE
AF:
0.0156
Gnomad4 OTH
AF:
0.00800
Alfa
AF:
0.00598
Hom.:
66

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs1555571892; hg19: chr17-59757841; API