rs4087296

Variant names:

• chr16-82344176-T-C
• rs4087296

Your query was ambiguous. Multiple possible variants found:

• chr16-82344176-T-C
• chr16-82344176-T-G

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 0.255 in 151,612 control chromosomes in the GnomAD database, including 5,693 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 (5693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 17 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 (AFR) allele frequency at 95% confidence interval = 0.399 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: 0.255 AC: 38614 AN: 151494 Hom.: 5685 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.255 AC: 38668 AN: 151612 Hom.: 5693 Cov.: 31 AF XY: 0.252 AC XY: 18669 AN XY: 74074

African (AFR) AF: 0.404 AC: 16665 AN: 41236

American (AMR) AF: 0.242 AC: 3691 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 893 AN: 3470

East Asian (EAS) AF: 0.302 AC: 1546 AN: 5120

South Asian (SAS) AF: 0.275 AC: 1318 AN: 4790

European-Finnish (FIN) AF: 0.123 AC: 1302 AN: 10552

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12531 AN: 67902

Other (OTH) AF: 0.240 AC: 506 AN: 2108

Alfa AF: 0.221 Hom.: 8025

Bravo AF: 0.271

Asia WGS AF: 0.295 AC: 1028 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	1.3
DANN	Benign	0.68
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4087296; hg19: chr16-82377781; COSMIC: COSV73978500;