22-27192801-T-A

Variant names:

• chr22-27192801-T-A
• rs864754

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 0.325 in 152,166 control chromosomes in the GnomAD database, including 8,298 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 0.33 (8298 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 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: 0.325 AC: 49479 AN: 152048 Hom.: 8291 Cov.: 33

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.325 AC: 49508 AN: 152166 Hom.: 8298 Cov.: 33 AF XY: 0.320 AC XY: 23814 AN XY: 74388

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.377

Alfa AF: 0.310 Hom.: 951

Bravo AF: 0.345

Asia WGS AF: 0.303 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.023
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs864754; hg19: chr22-27588763;