rs2180055

Variant names:

• chr22-48940611-C-T
• rs2180055

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 0.166 in 152,250 control chromosomes in the GnomAD database, including 2,604 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 0.17 (2604 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.166 AC: 25293 AN: 152132 Hom.: 2600 Cov.: 34

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.166 AC: 25340 AN: 152250 Hom.: 2604 Cov.: 34 AF XY: 0.169 AC XY: 12592 AN XY: 74444

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0617

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.146

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.172

Alfa AF: 0.121 Hom.: 794

Bravo AF: 0.171

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180055; hg19: chr22-49336423;