rs33942725

Variant names:

• chr16-87870933-G-C
• rs33942725

Your query was ambiguous. Multiple possible variants found:

• chr16-87870933-G-C
• chr16-87870933-G-T

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 0.186 in 152,176 control chromosomes in the GnomAD database, including 2,818 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 0.19 (2818 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.245 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: 0.186 AC: 28289 AN: 152058 Hom.: 2812 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.186 AC: 28311 AN: 152176 Hom.: 2818 Cov.: 32 AF XY: 0.184 AC XY: 13717 AN XY: 74386

African (AFR) AF: 0.145 AC: 6028 AN: 41518

American (AMR) AF: 0.154 AC: 2354 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3468

East Asian (EAS) AF: 0.138 AC: 715 AN: 5176

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4816

European-Finnish (FIN) AF: 0.154 AC: 1632 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14708 AN: 67990

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.0906 Hom.: 140

Bravo AF: 0.180

Asia WGS AF: 0.203 AC: 703 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	3.8
DANN	Benign	0.41
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs33942725; hg19: chr16-87904539;