rs11079786

Variant names:

• chr17-47728550-G-A
• rs11079786

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 0.274 in 151,978 control chromosomes in the GnomAD database, including 5,931 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 0.27 (5931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41585 AN: 151860 Hom.: 5934 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.274 AC: 41598 AN: 151978 Hom.: 5931 Cov.: 32 AF XY: 0.277 AC XY: 20568 AN XY: 74312

African (AFR) AF: 0.267 AC: 11056 AN: 41422

American (AMR) AF: 0.319 AC: 4883 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5176

South Asian (SAS) AF: 0.387 AC: 1863 AN: 4814

European-Finnish (FIN) AF: 0.295 AC: 3114 AN: 10570

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18226 AN: 67932

Other (OTH) AF: 0.270 AC: 569 AN: 2106

Alfa AF: 0.287 Hom.: 1022

Bravo AF: 0.275

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	0.43
DANN	Benign	0.65
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs11079786; hg19: chr17-45805916;