rs11228583

Variant names:

• chr11-69241647-G-T
• rs11228583

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 0.494 in 152,218 control chromosomes in the GnomAD database, including 19,622 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 0.49 (19622 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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 (AFR) allele frequency at 95% confidence interval = 0.578 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: 0.494 AC: 75167 AN: 152100 Hom.: 19584 Cov.: 34

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.0554

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.494 AC: 75256 AN: 152218 Hom.: 19622 Cov.: 34 AF XY: 0.488 AC XY: 36303 AN XY: 74436

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.0547

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.518

Alfa AF: 0.498 Hom.: 2375

Bravo AF: 0.494

Asia WGS AF: 0.282 AC: 982 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	2.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11228583; hg19: chr11-69009114;