chr18-60108063-G-A

Variant names:

• chr18-60108063-G-A
• rs9966951

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 0.341 in 151,854 control chromosomes in the GnomAD database, including 9,302 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 0.34 (9302 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51724 AN: 151736 Hom.: 9295 Cov.: 31

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.341 AC: 51763 AN: 151854 Hom.: 9302 Cov.: 31 AF XY: 0.337 AC XY: 25001 AN XY: 74210

African (AFR) AF: 0.434 AC: 17961 AN: 41410

American (AMR) AF: 0.279 AC: 4252 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.180 AC: 926 AN: 5158

South Asian (SAS) AF: 0.379 AC: 1818 AN: 4796

European-Finnish (FIN) AF: 0.265 AC: 2794 AN: 10536

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22029 AN: 67922

Other (OTH) AF: 0.331 AC: 697 AN: 2108

Alfa AF: 0.327 Hom.: 36217

Bravo AF: 0.344

Asia WGS AF: 0.249 AC: 865 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.45
DANN	Benign	0.68
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs9966951; hg19: chr18-57775295;