rs11232369

Positions:

• chr11-80851695-G-A

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 0.0571 in 152,022 control chromosomes in the GnomAD database, including 425 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 0.057 (425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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: 0.0570 AC: 8653 AN: 151904 Hom.: 423 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.0487

Gnomad SAS AF: 0.0204

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0299

Gnomad OTH AF: 0.0645

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

GnomAD4 genome AF: 0.0571 AC: 8673 AN: 152022 Hom.: 425 Cov.: 32 AF XY: 0.0566 AC XY: 4205 AN XY: 74300

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0329

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.0204

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0299

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0337 Hom.: 174

Bravo AF: 0.0601

Asia WGS AF: 0.0400 AC: 140 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11232369; hg19: chr11-80562738;