rs7933007

Variant names:

• chr11-118859960-C-T
• rs7933007

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;