rs2880494

Variant names:

• chr22-27486321-C-A
• rs2880494

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 0.295 in 151,852 control chromosomes in the GnomAD database, including 7,298 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 0.29 (7298 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36

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 (NFE) allele frequency at 95% confidence interval = 0.363 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: 0.295 AC: 44774 AN: 151734 Hom.: 7298 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.295 AC: 44779 AN: 151852 Hom.: 7298 Cov.: 32 AF XY: 0.295 AC XY: 21897 AN XY: 74174

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.293

Alfa AF: 0.352 Hom.: 19082

Bravo AF: 0.278

Asia WGS AF: 0.272 AC: 941 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2880494; hg19: chr22-27882282;