rs2052662

Variant names:

• chr18-73037973-A-G
• rs2052662

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.721 in 152,092 control chromosomes in the GnomAD database, including 40,643 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 0.72 (40643 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.832
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.803 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: 0.721 AC: 109605 AN: 151974 Hom.: 40635 Cov.: 33

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.751

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

GnomAD4 genome AF: 0.721 AC: 109653 AN: 152092 Hom.: 40643 Cov.: 33 AF XY: 0.719 AC XY: 53425 AN XY: 74346

African (AFR) AF: 0.539 AC: 22346 AN: 41460

American (AMR) AF: 0.751 AC: 11471 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3074 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3579 AN: 5170

South Asian (SAS) AF: 0.675 AC: 3256 AN: 4822

European-Finnish (FIN) AF: 0.788 AC: 8330 AN: 10574

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54973 AN: 67998

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.754 Hom.: 7644

Bravo AF: 0.712

Asia WGS AF: 0.674 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.74
DANN	Benign	0.79
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2052662; hg19: chr18-70705208;