rs7933202

Variant names:

• chr11-60169453-A-C
• rs7933202

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 0.279 in 152,100 control chromosomes in the GnomAD database, including 7,498 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 0.28 (7498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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: 0.279 AC: 42391 AN: 151982 Hom.: 7498 Cov.: 32

Gnomad AFR AF: 0.0805

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.279 AC: 42390 AN: 152100 Hom.: 7498 Cov.: 32 AF XY: 0.277 AC XY: 20593 AN XY: 74340

African (AFR) AF: 0.0804 AC: 3336 AN: 41506

American (AMR) AF: 0.279 AC: 4273 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1281 AN: 3464

East Asian (EAS) AF: 0.0688 AC: 356 AN: 5174

South Asian (SAS) AF: 0.456 AC: 2190 AN: 4804

European-Finnish (FIN) AF: 0.275 AC: 2907 AN: 10564

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26824 AN: 67982

Other (OTH) AF: 0.333 AC: 703 AN: 2112

Alfa AF: 0.320 Hom.: 1095

Bravo AF: 0.267

Asia WGS AF: 0.259 AC: 901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.28
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7933202; hg19: chr11-59936926;