rs690200

Positions:

• chr18-8908982-A-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 0.526 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;