rs4087296

chr16-82344176-T-Cchr16-82344176-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;