rs7929114

Variant names:

• chr11-45684612-A-G
• rs7929114

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 0.436 in 151,982 control chromosomes in the GnomAD database, including 14,931 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 0.44 (14931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.499 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: 0.436 AC: 66260 AN: 151866 Hom.: 14935 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.436 AC: 66264 AN: 151982 Hom.: 14931 Cov.: 32 AF XY: 0.430 AC XY: 31934 AN XY: 74268

African (AFR) AF: 0.350 AC: 14494 AN: 41438

American (AMR) AF: 0.351 AC: 5361 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1672 AN: 3472

East Asian (EAS) AF: 0.443 AC: 2278 AN: 5148

South Asian (SAS) AF: 0.496 AC: 2388 AN: 4818

European-Finnish (FIN) AF: 0.404 AC: 4276 AN: 10574

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34228 AN: 67946

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.483 Hom.: 76741

Bravo AF: 0.426

Asia WGS AF: 0.462 AC: 1605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs7929114; hg19: chr11-45706162;