rs16887552

Variant names:

• chr4-12772370-A-C
• rs16887552

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 0.3 in 152,112 control chromosomes in the GnomAD database, including 8,530 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 0.30 (8530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 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: 0.300 AC: 45531 AN: 151994 Hom.: 8500 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.300 AC: 45618 AN: 152112 Hom.: 8530 Cov.: 32 AF XY: 0.295 AC XY: 21906 AN XY: 74362

African (AFR) AF: 0.534 AC: 22102 AN: 41428

American (AMR) AF: 0.195 AC: 2978 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3470

East Asian (EAS) AF: 0.0574 AC: 297 AN: 5172

South Asian (SAS) AF: 0.210 AC: 1015 AN: 4822

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10600

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15237 AN: 67994

Other (OTH) AF: 0.271 AC: 573 AN: 2114

Alfa AF: 0.244 Hom.: 20240

Bravo AF: 0.304

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.0
DANN	Benign	0.27
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs16887552; hg19: chr4-12773994;