rs11079344

Variant names:

• chr17-58297122-A-G
• rs11079344

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 0.141 in 152,110 control chromosomes in the GnomAD database, including 2,195 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 0.14 (2195 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.285 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: 0.141 AC: 21380 AN: 151992 Hom.: 2184 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0761

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0751

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.141 AC: 21429 AN: 152110 Hom.: 2195 Cov.: 32 AF XY: 0.141 AC XY: 10465 AN XY: 74386

African (AFR) AF: 0.290 AC: 12010 AN: 41450

American (AMR) AF: 0.0936 AC: 1429 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.118 AC: 611 AN: 5180

South Asian (SAS) AF: 0.133 AC: 640 AN: 4816

European-Finnish (FIN) AF: 0.0761 AC: 806 AN: 10594

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0752 AC: 5111 AN: 68010

Other (OTH) AF: 0.130 AC: 274 AN: 2114

Alfa AF: 0.0914 Hom.: 855

Bravo AF: 0.148

Asia WGS AF: 0.107 AC: 374 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11079344; hg19: chr17-56374483;