rs2052662

Positions:

• chr18-73037973-A-G

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 0.721 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.539

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.692

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.808

Gnomad4 OTH AF: 0.752

Alfa AF: 0.761 Hom.: 7538

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2052662; hg19: chr18-70705208;