rs9927153

Variant names:

• chr16-81436413-C-T
• rs9927153

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 0.225 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.216 AC: 8964 AN: 41486

American (AMR) AF: 0.195 AC: 2981 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 773 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1694 AN: 5164

South Asian (SAS) AF: 0.280 AC: 1348 AN: 4814

European-Finnish (FIN) AF: 0.211 AC: 2235 AN: 10574

Middle Eastern (MID) AF: 0.298 AC: 87 AN: 292

European-Non Finnish (NFE) AF: 0.229 AC: 15534 AN: 67976

Other (OTH) AF: 0.245 AC: 517 AN: 2112

Alfa AF: 0.229 Hom.: 16683

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
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs9927153; hg19: chr16-81470018;