rs1942873

chr18-60188653-G-C

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 0.812 in 152,090 control chromosomes in the GnomAD database, including 50,320 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 0.81 (50320 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.812 AC: 123365 AN: 151972 Hom.: 50280 Cov.: 31

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.917

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.812 AC: 123461 AN: 152090 Hom.: 50320 Cov.: 31 AF XY: 0.813 AC XY: 60435 AN XY: 74338

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.881

Gnomad4 FIN AF: 0.757

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.826

Alfa AF: 0.799 Hom.: 6055

Bravo AF: 0.820

Asia WGS AF: 0.911 AC: 3170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.74
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1942873; hg19: chr18-57855886;