rs11659028

chr17-43043008-T-Achr17-43043008-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 id is 209228.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43043008-T-A is described in Lovd as [Benign].
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.272

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.332

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

Benign, reviewed by expert panel

curation

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

Jan 12, 2015

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11659028; hg19: chr17-41195025;