rs11086243

Variant names:

• chr20-48150492-C-T
• rs11086243

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 0.427 in 152,118 control chromosomes in the GnomAD database, including 14,452 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 0.43 (14452 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.20
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.494 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: 0.427 AC: 64936 AN: 152000 Hom.: 14436 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.427 AC: 64983 AN: 152118 Hom.: 14452 Cov.: 33 AF XY: 0.424 AC XY: 31566 AN XY: 74370

African (AFR) AF: 0.330 AC: 13708 AN: 41496

American (AMR) AF: 0.422 AC: 6446 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3472

East Asian (EAS) AF: 0.223 AC: 1157 AN: 5180

South Asian (SAS) AF: 0.383 AC: 1848 AN: 4828

European-Finnish (FIN) AF: 0.498 AC: 5265 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.498 AC: 33872 AN: 67974

Other (OTH) AF: 0.404 AC: 854 AN: 2112

Alfa AF: 0.459 Hom.: 28981

Bravo AF: 0.414

Asia WGS AF: 0.319 AC: 1111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0020
DANN	Benign	0.61
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs11086243; hg19: chr20-46779235;