rs9951586

Variant names:

• chr18-77145362-C-T
• rs9951586

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 0.688 in 152,168 control chromosomes in the GnomAD database, including 37,595 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 0.69 (37595 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104573 AN: 152050 Hom.: 37568 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.801

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.688 AC: 104655 AN: 152168 Hom.: 37595 Cov.: 33 AF XY: 0.688 AC XY: 51172 AN XY: 74382

African (AFR) AF: 0.463 AC: 19210 AN: 41486

American (AMR) AF: 0.738 AC: 11286 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3470

East Asian (EAS) AF: 0.738 AC: 3815 AN: 5172

South Asian (SAS) AF: 0.604 AC: 2917 AN: 4830

European-Finnish (FIN) AF: 0.779 AC: 8252 AN: 10590

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.801 AC: 54476 AN: 68008

Other (OTH) AF: 0.695 AC: 1467 AN: 2110

Alfa AF: 0.762 Hom.: 186616

Bravo AF: 0.674

Asia WGS AF: 0.621 AC: 2160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.83
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9951586; hg19: chr18-74857318;