rs864754

Positions:

• chr22-27192801-T-A
• chr22-27192801-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 0.325 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;