17-61680480-C-CTTTCTTTT

Position:

• chr17-61680480-C-CTTTCTTTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

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 -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
BRIP1	NM_032043.3	c.*2815_*2816insAAAAGAAA		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.*2815_*2816insAAAAGAAA		3_prime_UTR_variant	20/20	1	NM_032043.3	ENSP00000259008.2
BRIP1	ENST00000682755	c.*2815_*2816insAAAAGAAA		3_prime_UTR_variant	18/18			ENSP00000507660.1

Frequencies

GnomAD3 genomes AF: 0.0123 AC: 1521 AN: 124026 Hom.: 47 Cov.: 0

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

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555571892; hg19: chr17-59757841;