rs408199

Variant names:

• chr11-22605073-C-T
• rs408199

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;