rs11228583

Positions:

• chr11-69241647-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;