rs11659028

Variant names:

• chr17-43043008-T-A
• rs11659028

Your query was ambiguous. Multiple possible variants found:

• chr17-43043008-T-A
• chr17-43043008-T-G

Variant summary

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

The variant allele was found at a frequency of 0.311 in 151,650 control chromosomes in the GnomAD database, including 7,700 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.31 (7700 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign reviewed by expert panel B:1
• Conservation: PhyloP100: 0.0620
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 17-43043008-T-A is Benign according to our data. Variant chr17-43043008-T-A is described in ClinVar as Benign. ClinVar VariationId is 209228.Status of the report is reviewed_by_expert_panel, 3 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47121 AN: 151532 Hom.: 7697 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.311 AC: 47141 AN: 151650 Hom.: 7700 Cov.: 31 AF XY: 0.317 AC XY: 23445 AN XY: 74066

African (AFR) AF: 0.232 AC: 9608 AN: 41344

American (AMR) AF: 0.272 AC: 4148 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1891 AN: 5118

South Asian (SAS) AF: 0.492 AC: 2371 AN: 4818

European-Finnish (FIN) AF: 0.408 AC: 4273 AN: 10482

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22542 AN: 67866

Other (OTH) AF: 0.332 AC: 699 AN: 2108

Alfa AF: 0.313 Hom.: 999

Bravo AF: 0.291

Asia WGS AF: 0.414 AC: 1439 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: reviewed by expert panel

Submissions by phenotype

Breast-ovarian cancer, familial, susceptibility to, 1 Benign:1

Jan 12, 2015

Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)

Significance: Benign

Review Status: reviewed by expert panel

Collection Method: curation

Class 1 not pathogenic based on frequency >1% in an outbred sampleset. Frequency 0.33 (Asian), 0.22 (African), 0.36 (European), derived from 1000 genomes (2012-04-30). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.83
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs11659028; hg19: chr17-41195025;