rs16887552

Positions:

• chr4-12772370-A-C

Variant summary

Our verdict is Benign. Variant got -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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.605

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.12772370A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0574

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.271

Alfa AF: 0.232 Hom.: 7427

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16887552; hg19: chr4-12773994;