rs33988046

Variant names:

• chr16-87870620-G-A
• rs33988046

Your query was ambiguous. Multiple possible variants found:

• chr16-87870620-G-A
• chr16-87870620-G-C

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 0.0684 in 152,276 control chromosomes in the GnomAD database, including 412 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 0.068 (412 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0835 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: 0.0683 AC: 10391 AN: 152158 Hom.: 408 Cov.: 33

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0868

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0816

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.0674

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

GnomAD4 genome AF: 0.0684 AC: 10412 AN: 152276 Hom.: 412 Cov.: 33 AF XY: 0.0673 AC XY: 5008 AN XY: 74450

African (AFR) AF: 0.0858 AC: 3565 AN: 41542

American (AMR) AF: 0.0865 AC: 1323 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0398 AC: 138 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5186

South Asian (SAS) AF: 0.0811 AC: 391 AN: 4822

European-Finnish (FIN) AF: 0.0370 AC: 393 AN: 10618

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4358 AN: 68022

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0315 Hom.: 18

Bravo AF: 0.0744

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	6.7
DANN	Benign	0.39
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs33988046; hg19: chr16-87904226;