rs10515211

chr17-61800589-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032043.3(BRIP1):c.1140+664T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,186 control chromosomes in the GnomAD database, including 3,758 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3758 hom., cov: 32)
• Consequence: BRIP1 NM_032043.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRIP1	NM_032043.3	c.1140+664T>C		intron_variant		ENST00000259008.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRIP1	ENST00000259008.7	c.1140+664T>C		intron_variant		1	NM_032043.3	P2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30113 AN: 152068 Hom.: 3746 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.198 AC: 30144 AN: 152186 Hom.: 3758 Cov.: 32 AF XY: 0.200 AC XY: 14850 AN XY: 74412

Gnomad4 AFR AF: 0.0723

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.169

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.222

Alfa AF: 0.233 Hom.: 1008

Bravo AF: 0.210

Asia WGS AF: 0.190 AC: 662 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.5
Dann	Benign	0.84

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: rs10515211; hg19: chr17-59877950;