chr17-43039112-G-T

Variant names:

• chr17-43039112-G-T
• rs11657053

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.31 in 152,056 control chromosomes in the GnomAD database, including 7,698 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (7698 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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: 0.310 AC: 47147 AN: 151938 Hom.: 7696 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.310 AC: 47166 AN: 152056 Hom.: 7698 Cov.: 32 AF XY: 0.316 AC XY: 23452 AN XY: 74292

African (AFR) AF: 0.232 AC: 9605 AN: 41476

American (AMR) AF: 0.271 AC: 4141 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3468

East Asian (EAS) AF: 0.369 AC: 1911 AN: 5174

South Asian (SAS) AF: 0.493 AC: 2378 AN: 4822

European-Finnish (FIN) AF: 0.404 AC: 4261 AN: 10540

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

European-Non Finnish (NFE) AF: 0.332 AC: 22551 AN: 67986

Other (OTH) AF: 0.332 AC: 699 AN: 2106

Alfa AF: 0.319 Hom.: 23710

Bravo AF: 0.291

Asia WGS AF: 0.407 AC: 1414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.1
DANN	Benign	0.36
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs11657053; hg19: chr17-41191129;