rs9932186

chr16-60280752-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.0809

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.161

Alfa AF: 0.190 Hom.: 3177

Bravo AF: 0.141

Asia WGS AF: 0.0910 AC: 317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9932186; hg19: chr16-60314656;