rs408199

chr11-22605073-C-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 0.683 in 151,864 control chromosomes in the GnomAD database, including 36,533 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 0.68 (36533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 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: 0.683 AC: 103653 AN: 151746 Hom.: 36542 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.683 AC: 103667 AN: 151864 Hom.: 36533 Cov.: 32 AF XY: 0.678 AC XY: 50305 AN XY: 74200

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.699

Alfa AF: 0.763 Hom.: 23917

Bravo AF: 0.680

Asia WGS AF: 0.514 AC: 1786 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs408199; hg19: chr11-22626619;