rs11224899

Variant names:

• chr11-97088525-G-A
• rs11224899

Your query was ambiguous. Multiple possible variants found:

• chr11-97088525-G-A
• chr11-97088525-G-T

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 0.0623 in 151,968 control chromosomes in the GnomAD database, including 421 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 0.062 (421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.0623 AC: 9455 AN: 151850 Hom.: 418 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0422

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.0475

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0639

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

GnomAD4 genome AF: 0.0623 AC: 9471 AN: 151968 Hom.: 421 Cov.: 32 AF XY: 0.0650 AC XY: 4826 AN XY: 74282

African (AFR) AF: 0.101 AC: 4178 AN: 41474

American (AMR) AF: 0.0422 AC: 644 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 350 AN: 3466

East Asian (EAS) AF: 0.214 AC: 1101 AN: 5154

South Asian (SAS) AF: 0.0471 AC: 227 AN: 4820

European-Finnish (FIN) AF: 0.0509 AC: 537 AN: 10560

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0322 AC: 2186 AN: 67936

Other (OTH) AF: 0.0642 AC: 135 AN: 2104

Alfa AF: 0.0454 Hom.: 298

Bravo AF: 0.0641

Asia WGS AF: 0.118 AC: 411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs11224899; hg19: chr11-96959525;