rs33923136

Variant names:

• chr16-87870949-A-G
• rs33923136

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 0.177 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.115 AC: 4793 AN: 41532

American (AMR) AF: 0.149 AC: 2277 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3468

East Asian (EAS) AF: 0.138 AC: 714 AN: 5168

South Asian (SAS) AF: 0.257 AC: 1242 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1630 AN: 10594

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14708 AN: 67978

Other (OTH) AF: 0.196 AC: 414 AN: 2110

Alfa AF: 0.187 Hom.: 368

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
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs33923136; hg19: chr16-87904555;