16-60280752-G-T

Variant names:

• chr16-60280752-G-T
• rs9932186

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 0.143 in 152,042 control chromosomes in the GnomAD database, including 1,803 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 0.14 (1803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675
• Publications: 8 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 = 0.196 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: 0.143 AC: 21712 AN: 151926 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.0634

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0811

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.143 AC: 21708 AN: 152042 Hom.: 1803 Cov.: 32 AF XY: 0.138 AC XY: 10231 AN XY: 74308

African (AFR) AF: 0.0632 AC: 2624 AN: 41502

American (AMR) AF: 0.124 AC: 1895 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3468

East Asian (EAS) AF: 0.0809 AC: 417 AN: 5154

South Asian (SAS) AF: 0.125 AC: 601 AN: 4810

European-Finnish (FIN) AF: 0.135 AC: 1426 AN: 10548

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13501 AN: 67990

Other (OTH) AF: 0.161 AC: 338 AN: 2098

Alfa AF: 0.185 Hom.: 8067

Bravo AF: 0.141

Asia WGS AF: 0.0910 AC: 317 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	8.5
DANN	Benign	0.60
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs9932186; hg19: chr16-60314656;