16-87870886-G-A

Variant names:

• chr16-87870886-G-A
• rs33914778

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 0.428 in 152,034 control chromosomes in the GnomAD database, including 14,915 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 0.43 (14915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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: 0.428 AC: 64989 AN: 151916 Hom.: 14878 Cov.: 33

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.428 AC: 65070 AN: 152034 Hom.: 14915 Cov.: 33 AF XY: 0.422 AC XY: 31342 AN XY: 74318

African (AFR) AF: 0.595 AC: 24641 AN: 41438

American (AMR) AF: 0.328 AC: 5009 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1235 AN: 3472

East Asian (EAS) AF: 0.144 AC: 748 AN: 5178

South Asian (SAS) AF: 0.394 AC: 1900 AN: 4822

European-Finnish (FIN) AF: 0.326 AC: 3443 AN: 10576

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26771 AN: 67966

Other (OTH) AF: 0.402 AC: 849 AN: 2112

Alfa AF: 0.289 Hom.: 700

Bravo AF: 0.432

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	6.0
DANN	Benign	0.58
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs33914778; hg19: chr16-87904492;