rs7223952

chr17-43042868-T-C

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 0.446 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

ACMG classification

Verdict is Benign. Variant got -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 id is 209227.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr17-43042868-T-C is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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: 0.446 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

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.424

Alfa AF: 0.387 Hom.: 4116

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

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), 0.72 (African), 0.37 (European), derived from 1000 genomes (2012-04-30). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7223952; hg19: chr17-41194885;