rs7213430

Variant names:

• chr17-61682813-G-A
• rs7213430
• NM_032043.3:c.*483C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-61682813-G-A
• chr17-61682813-G-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_032043.3(BRIP1):​c.*483C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.612 in 191,258 control chromosomes in the GnomAD database, including 36,575 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.61 (28954 hom., cov: 32)
  • Exomes 𝑓: 0.62 (7621 hom.)
• Consequence: BRIP1 NM_032043.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -0.0250
• Publications: 16 publications found

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: Illumina, Orphanet
• Fanconi anemia complementation group J

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: STRONG, LIMITED, NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics, ClinGen
• colorectal adenoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 17-61682813-G-A is Benign according to our data. Variant chr17-61682813-G-A is described in ClinVar as Benign. ClinVar VariationId is 324335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032043.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRIP1	NM_032043.3	MANE Select	c.*483C>T		3_prime_UTR	Exon 20 of 20	NP_114432.2	Q9BX63-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRIP1	ENST00000259008.7	TSL:1 MANE Select	c.*483C>T		3_prime_UTR	Exon 20 of 20	ENSP00000259008.2	Q9BX63-1
	BRIP1	ENST00000682453.1		c.*483C>T		3_prime_UTR	Exon 21 of 21	ENSP00000506943.1	Q9BX63-1
	BRIP1	ENST00000683039.1		c.*483C>T		3_prime_UTR	Exon 21 of 21	ENSP00000508303.1	Q9BX63-1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92718 AN: 151952 Hom.: 28915 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 0.618 AC: 24215 AN: 39186 Hom.: 7621 Cov.: 0 AF XY: 0.613 AC XY: 11233 AN XY: 18338

African (AFR) AF: 0.646 AC: 958 AN: 1482

American (AMR) AF: 0.741 AC: 922 AN: 1244

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1390 AN: 2422

East Asian (EAS) AF: 0.760 AC: 4960 AN: 6524

South Asian (SAS) AF: 0.403 AC: 196 AN: 486

European-Finnish (FIN) AF: 0.526 AC: 20 AN: 38

Middle Eastern (MID) AF: 0.646 AC: 146 AN: 226

European-Non Finnish (NFE) AF: 0.583 AC: 13771 AN: 23628

Other (OTH) AF: 0.591 AC: 1852 AN: 3136

GnomAD4 genome AF: 0.610 AC: 92819 AN: 152072 Hom.: 28954 Cov.: 32 AF XY: 0.605 AC XY: 44944 AN XY: 74324

African (AFR) AF: 0.670 AC: 27780 AN: 41474

American (AMR) AF: 0.737 AC: 11262 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2035 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3735 AN: 5180

South Asian (SAS) AF: 0.460 AC: 2215 AN: 4820

European-Finnish (FIN) AF: 0.408 AC: 4312 AN: 10560

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.583 AC: 39618 AN: 67978

Other (OTH) AF: 0.630 AC: 1331 AN: 2112

Alfa AF: 0.601 Hom.: 28934

Bravo AF: 0.641

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Fanconi anemia complementation group J (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.28
PhyloP100		-0.025
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

Other links and lift over

dbSNP: rs7213430; hg19: chr17-59760174;