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. Variant got -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

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 (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

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.240

Alfa AF: 0.201 Hom.: 3778

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

Splicing

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

Publications

LitVar

Other links and lift over

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