16-52878826-C-G

Variant names:

• chr16-52878826-C-G
• rs8056052

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 0.429 in 152,104 control chromosomes in the GnomAD database, including 14,117 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 (14117 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65220 AN: 151986 Hom.: 14095 Cov.: 33

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.429 AC: 65271 AN: 152104 Hom.: 14117 Cov.: 33 AF XY: 0.428 AC XY: 31831 AN XY: 74352

African (AFR) AF: 0.447 AC: 18537 AN: 41498

American (AMR) AF: 0.483 AC: 7384 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3466

East Asian (EAS) AF: 0.598 AC: 3092 AN: 5172

South Asian (SAS) AF: 0.419 AC: 2021 AN: 4820

European-Finnish (FIN) AF: 0.416 AC: 4394 AN: 10568

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27368 AN: 67974

Other (OTH) AF: 0.417 AC: 881 AN: 2112

Alfa AF: 0.271 Hom.: 622

Bravo AF: 0.442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.56
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs8056052; hg19: chr16-52912738;