rs7929114

chr11-45684612-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;