rs7929114

Variant names:

• chr11-45684612-A-G
• rs7929114

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.436 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

Gnomad4 AFR AF: 0.350

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.433

Alfa AF: 0.491 Hom.: 38308

Bravo AF: 0.426

Asia WGS AF: 0.462 AC: 1605 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7929114; hg19: chr11-45706162;