rs3849233

Positions:

• chr16-87047584-A-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 0.315 in 151,994 control chromosomes in the GnomAD database, including 9,205 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 0.31 (9205 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47814 AN: 151876 Hom.: 9205 Cov.: 32

Gnomad AFR AF: 0.0863

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.315 AC: 47812 AN: 151994 Hom.: 9205 Cov.: 32 AF XY: 0.318 AC XY: 23604 AN XY: 74270

Gnomad4 AFR AF: 0.0861

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.326

Alfa AF: 0.398 Hom.: 17034

Bravo AF: 0.293

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3849233; hg19: chr16-87081190;