22-27456222-T-C

Position:

• chr22-27456222-T-C

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 0.0947 in 152,204 control chromosomes in the GnomAD database, including 679 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 0.095 (679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.135 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: 0.0948 AC: 14413 AN: 152086 Hom.: 680 Cov.: 32

Gnomad AFR AF: 0.0681

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0861

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0965

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0947 AC: 14409 AN: 152204 Hom.: 679 Cov.: 32 AF XY: 0.0928 AC XY: 6907 AN XY: 74418

Gnomad4 AFR AF: 0.0679

Gnomad4 AMR AF: 0.0860

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0965

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0768

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.0994

Alfa AF: 0.110 Hom.: 2127

Bravo AF: 0.0917

Asia WGS AF: 0.115 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6005451; hg19: chr22-27852183; COSMIC: COSV71131613;