rs9927153

chr16-81436413-C-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 0.225 in 152,080 control chromosomes in the GnomAD database, including 3,867 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 0.23 (3867 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.315 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: 0.225 AC: 34236 AN: 151962 Hom.: 3859 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.225 AC: 34268 AN: 152080 Hom.: 3867 Cov.: 32 AF XY: 0.226 AC XY: 16819 AN XY: 74332

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.245

Alfa AF: 0.232 Hom.: 8166

Bravo AF: 0.221

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.81
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9927153; hg19: chr16-81470018;