rs11212733

Positions:

• chr11-108608096-T-A
• chr11-108608096-T-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 0.515 in 152,054 control chromosomes in the GnomAD database, including 20,467 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 0.51 (20467 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.108608096T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78217 AN: 151936 Hom.: 20437 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.515 AC: 78297 AN: 152054 Hom.: 20467 Cov.: 32 AF XY: 0.515 AC XY: 38310 AN XY: 74340

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.520

Alfa AF: 0.487 Hom.: 2261

Bravo AF: 0.522

Asia WGS AF: 0.632 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11212733; hg19: chr11-108478823;