18-60191833-A-G

Variant names:

• chr18-60191833-A-G
• rs619825

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 0.467 in 152,006 control chromosomes in the GnomAD database, including 18,718 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 0.47 (18718 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.113

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.716 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: 0.466 AC: 70834 AN: 151888 Hom.: 18673 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.467 AC: 70931 AN: 152006 Hom.: 18718 Cov.: 32 AF XY: 0.459 AC XY: 34128 AN XY: 74304

Gnomad4 AFR AF: 0.723

Gnomad4 AMR AF: 0.325

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.431

Alfa AF: 0.394 Hom.: 12131

Bravo AF: 0.474

Asia WGS AF: 0.343 AC: 1193 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	5.6
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs619825; hg19: chr18-57859066;