17-43042868-T-C

Variant names:

• chr17-43042868-T-C
• rs7223952

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 0.446 in 152,002 control chromosomes in the GnomAD database, including 17,012 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★★).

• Frequency: Genomes: 𝑓 0.45 (17012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign reviewed by expert panel B:1
• Conservation: PhyloP100: -0.516
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 17-43042868-T-C is Benign according to our data. Variant chr17-43042868-T-C is described in ClinVar as Benign. ClinVar VariationId is 209227.Status of the report is reviewed_by_expert_panel, 3 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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: 0.446 AC: 67695 AN: 151884 Hom.: 16968 Cov.: 32

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.446 AC: 67786 AN: 152002 Hom.: 17012 Cov.: 32 AF XY: 0.447 AC XY: 33203 AN XY: 74276

African (AFR) AF: 0.687 AC: 28469 AN: 41466

American (AMR) AF: 0.319 AC: 4863 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1907 AN: 5178

South Asian (SAS) AF: 0.522 AC: 2510 AN: 4804

European-Finnish (FIN) AF: 0.407 AC: 4298 AN: 10564

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.341 AC: 23201 AN: 67944

Other (OTH) AF: 0.424 AC: 895 AN: 2112

Alfa AF: 0.386 Hom.: 5034

Bravo AF: 0.444

Asia WGS AF: 0.462 AC: 1607 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), 0.72 (African), 0.37 (European), derived from 1000 genomes (2012-04-30).

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7223952; hg19: chr17-41194885;