chr17-43043694-G-C

Variant names:

• chr17-43043694-G-C
• rs8176323

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 0.31 in 152,082 control chromosomes in the GnomAD database, including 7,714 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.31 (7714 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign reviewed by expert panel B:1
• Conservation: PhyloP100: -0.295
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 17-43043694-G-C is Benign according to our data. Variant chr17-43043694-G-C is described in ClinVar as Benign. ClinVar VariationId is 209230.Status of the report is reviewed_by_expert_panel, 3 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47193 AN: 151964 Hom.: 7711 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.310 AC: 47213 AN: 152082 Hom.: 7714 Cov.: 32 AF XY: 0.316 AC XY: 23492 AN XY: 74350

African (AFR) AF: 0.232 AC: 9624 AN: 41490

American (AMR) AF: 0.272 AC: 4150 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3472

East Asian (EAS) AF: 0.369 AC: 1909 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2377 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4272 AN: 10566

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22569 AN: 67962

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.313 Hom.: 947

Bravo AF: 0.291

Asia WGS AF: 0.415 AC: 1442 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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.56
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs8176323; hg19: chr17-41195711;