16-87871263-A-G

Variant names:

• chr16-87871263-A-G
• rs33916661

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 0.257 in 152,102 control chromosomes in the GnomAD database, including 5,339 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 0.26 (5339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.257 AC: 39033 AN: 151984 Hom.: 5322 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.257 AC: 39087 AN: 152102 Hom.: 5339 Cov.: 32 AF XY: 0.254 AC XY: 18894 AN XY: 74368

African (AFR) AF: 0.345 AC: 14288 AN: 41464

American (AMR) AF: 0.187 AC: 2860 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1014 AN: 3468

East Asian (EAS) AF: 0.138 AC: 716 AN: 5178

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4822

European-Finnish (FIN) AF: 0.178 AC: 1891 AN: 10596

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16148 AN: 67982

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.242 Hom.: 3206

Bravo AF: 0.257

Asia WGS AF: 0.227 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.65
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs33916661; hg19: chr16-87904869;