rs33923136

chr16-87870949-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 0.177 in 152,158 control chromosomes in the GnomAD database, including 2,660 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 0.18 (2660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 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: 0.177 AC: 26965 AN: 152040 Hom.: 2657 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.177 AC: 26975 AN: 152158 Hom.: 2660 Cov.: 32 AF XY: 0.176 AC XY: 13101 AN XY: 74382

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.196

Alfa AF: 0.189 Hom.: 282

Bravo AF: 0.170

Asia WGS AF: 0.199 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
Cadd	Benign	2.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33923136; hg19: chr16-87904555;