17-11046080-C-G

Variant names:

• chr17-11046080-C-G
• rs2079571

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 0.924 in 152,240 control chromosomes in the GnomAD database, including 65,113 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 0.92 (65113 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140578 AN: 152122 Hom.: 65052 Cov.: 31

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.924 AC: 140698 AN: 152240 Hom.: 65113 Cov.: 31 AF XY: 0.925 AC XY: 68850 AN XY: 74434

African (AFR) AF: 0.968 AC: 40211 AN: 41552

American (AMR) AF: 0.935 AC: 14287 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3068 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5166 AN: 5176

South Asian (SAS) AF: 0.855 AC: 4119 AN: 4816

European-Finnish (FIN) AF: 0.922 AC: 9777 AN: 10604

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.899 AC: 61115 AN: 68014

Other (OTH) AF: 0.906 AC: 1915 AN: 2114

Alfa AF: 0.913 Hom.: 7384

Bravo AF: 0.929

Asia WGS AF: 0.935 AC: 3250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.39
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs2079571; hg19: chr17-10949397;