chr11-2207722-C-A

Position:

• chr11-2207722-C-A

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 0.74 in 152,018 control chromosomes in the GnomAD database, including 42,488 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 0.74 (42488 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112517 AN: 151900 Hom.: 42491 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.740 AC: 112553 AN: 152018 Hom.: 42488 Cov.: 32 AF XY: 0.741 AC XY: 55050 AN XY: 74298

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.746

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.781

Alfa AF: 0.783 Hom.: 8233

Bravo AF: 0.732

Asia WGS AF: 0.800 AC: 2783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.068
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7126629; hg19: chr11-2228952;