rs722490

Variant names:

• chr11-22555272-G-A
• rs722490

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 0.157 in 151,984 control chromosomes in the GnomAD database, including 2,232 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 0.16 (2232 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 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: 0.157 AC: 23887 AN: 151866 Hom.: 2231 Cov.: 33

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.157 AC: 23892 AN: 151984 Hom.: 2232 Cov.: 33 AF XY: 0.160 AC XY: 11881 AN XY: 74288

African (AFR) AF: 0.0773 AC: 3205 AN: 41480

American (AMR) AF: 0.102 AC: 1563 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3466

East Asian (EAS) AF: 0.222 AC: 1146 AN: 5166

South Asian (SAS) AF: 0.108 AC: 519 AN: 4808

European-Finnish (FIN) AF: 0.299 AC: 3159 AN: 10548

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13107 AN: 67940

Other (OTH) AF: 0.165 AC: 347 AN: 2108

Alfa AF: 0.173 Hom.: 1411

Bravo AF: 0.140

Asia WGS AF: 0.172 AC: 598 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	8.0
DANN	Benign	0.72
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs722490; hg19: chr11-22576818;