rs7935502

Variant names:

• chr11-88428828-G-A
• rs7935502

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 0.248 in 152,082 control chromosomes in the GnomAD database, including 5,176 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 0.25 (5176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 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: 0.248 AC: 37720 AN: 151964 Hom.: 5182 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.248 AC: 37702 AN: 152082 Hom.: 5176 Cov.: 32 AF XY: 0.240 AC XY: 17828 AN XY: 74336

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.277

Alfa AF: 0.311 Hom.: 15179

Bravo AF: 0.248

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.70
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: rs7935502; hg19: chr11-88161996;