chr18-8908982-A-C

Variant names:

• chr18-8908982-A-C
• rs690200

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.396 AC: 16429 AN: 41450

American (AMR) AF: 0.484 AC: 7390 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3457 AN: 5152

South Asian (SAS) AF: 0.387 AC: 1862 AN: 4816

European-Finnish (FIN) AF: 0.696 AC: 7360 AN: 10574

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39328 AN: 67948

Other (OTH) AF: 0.543 AC: 1147 AN: 2112

Alfa AF: 0.535 Hom.: 22547

Bravo AF: 0.510

Asia WGS AF: 0.500 AC: 1738 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.55
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs690200; hg19: chr18-8908980;