18-55153893-A-G

Variant names:

• chr18-55153893-A-G
• rs9951150

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 0.508 in 151,900 control chromosomes in the GnomAD database, including 20,429 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 0.51 (20429 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.66 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: 0.508 AC: 77127 AN: 151782 Hom.: 20405 Cov.: 31

Gnomad AFR AF: 0.667

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.508 AC: 77203 AN: 151900 Hom.: 20429 Cov.: 31 AF XY: 0.503 AC XY: 37307 AN XY: 74238

African (AFR) AF: 0.666 AC: 27601 AN: 41412

American (AMR) AF: 0.473 AC: 7227 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.464 AC: 1606 AN: 3464

East Asian (EAS) AF: 0.327 AC: 1685 AN: 5146

South Asian (SAS) AF: 0.508 AC: 2446 AN: 4812

European-Finnish (FIN) AF: 0.410 AC: 4326 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30910 AN: 67930

Other (OTH) AF: 0.489 AC: 1031 AN: 2110

Alfa AF: 0.466 Hom.: 58823

Bravo AF: 0.518

Asia WGS AF: 0.461 AC: 1600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.051
DANN	Benign	0.71
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9951150; hg19: chr18-52821124;