rs2180055

Positions:

• chr22-48940611-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;