22-40685223-G-T

Variant names:

• chr22-40685223-G-T
• rs882111

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 0.0517 in 152,234 control chromosomes in the GnomAD database, including 271 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 0.052 (271 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 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: 0.0517 AC: 7872 AN: 152116 Hom.: 271 Cov.: 31

Gnomad AFR AF: 0.0179

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0656

Gnomad ASJ AF: 0.0472

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0219

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0667

Gnomad OTH AF: 0.0466

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

GnomAD4 genome AF: 0.0517 AC: 7874 AN: 152234 Hom.: 271 Cov.: 31 AF XY: 0.0514 AC XY: 3822 AN XY: 74422

Gnomad4 AFR AF: 0.0179

Gnomad4 AMR AF: 0.0656

Gnomad4 ASJ AF: 0.0472

Gnomad4 EAS AF: 0.0838

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0219

Gnomad4 NFE AF: 0.0667

Gnomad4 OTH AF: 0.0466

Alfa AF: 0.0600 Hom.: 303

Bravo AF: 0.0504

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs882111; hg19: chr22-41081227;