rs690200

Variant names:

• chr18-8908982-A-C
• rs690200

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 0.526 in 151,990 control chromosomes in the GnomAD database, including 21,844 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 0.53 (21844 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.526 AC: 79893 AN: 151874 Hom.: 21843 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.526 AC: 79934 AN: 151990 Hom.: 21844 Cov.: 32 AF XY: 0.528 AC XY: 39249 AN XY: 74306

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.543

Alfa AF: 0.550 Hom.: 13294

Bravo AF: 0.510

Asia WGS AF: 0.500 AC: 1738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs690200; hg19: chr18-8908980;