rs11683087

Variant names:

• chr2-226721890-G-A
• rs11683087

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 0.621 in 152,086 control chromosomes in the GnomAD database, including 34,495 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 0.62 (34495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.805 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: 0.621 AC: 94439 AN: 151968 Hom.: 34494 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.663

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.621 AC: 94449 AN: 152086 Hom.: 34495 Cov.: 32 AF XY: 0.623 AC XY: 46274 AN XY: 74334

African (AFR) AF: 0.206 AC: 8544 AN: 41454

American (AMR) AF: 0.664 AC: 10142 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.796 AC: 2762 AN: 3468

East Asian (EAS) AF: 0.706 AC: 3651 AN: 5172

South Asian (SAS) AF: 0.698 AC: 3364 AN: 4818

European-Finnish (FIN) AF: 0.809 AC: 8560 AN: 10578

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55133 AN: 68002

Other (OTH) AF: 0.685 AC: 1446 AN: 2110

Alfa AF: 0.745 Hom.: 81957

Bravo AF: 0.589

Asia WGS AF: 0.686 AC: 2386 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.9
DANN	Benign	0.66
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs11683087; hg19: chr2-227586606;