chr11-22605073-C-T

Variant names:

• chr11-22605073-C-T
• rs408199

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 0.683 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.527 AC: 21802 AN: 41370

American (AMR) AF: 0.758 AC: 11560 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1809 AN: 5150

South Asian (SAS) AF: 0.763 AC: 3675 AN: 4816

European-Finnish (FIN) AF: 0.657 AC: 6916 AN: 10532

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52830 AN: 67962

Other (OTH) AF: 0.699 AC: 1474 AN: 2110

Alfa AF: 0.759 Hom.: 32360

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs408199; hg19: chr11-22626619;