rs7933007

Positions:

• chr11-118859960-C-T

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 0.783 in 152,028 control chromosomes in the GnomAD database, including 46,903 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 0.78 (46903 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118979 AN: 151912 Hom.: 46842 Cov.: 30

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.848

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.783 AC: 119100 AN: 152028 Hom.: 46903 Cov.: 30 AF XY: 0.779 AC XY: 57863 AN XY: 74316

Gnomad4 AFR AF: 0.847

Gnomad4 AMR AF: 0.848

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.791

Alfa AF: 0.759 Hom.: 24727

Bravo AF: 0.801

Asia WGS AF: 0.661 AC: 2299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.81
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7933007; hg19: chr11-118730669;