16-84806348-C-A

Variant names:

• chr16-84806348-C-A
• rs8057431

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 0.776 in 151,960 control chromosomes in the GnomAD database, including 46,028 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 0.78 (46028 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 26 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117738 AN: 151842 Hom.: 45964 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.776 AC: 117860 AN: 151960 Hom.: 46028 Cov.: 30 AF XY: 0.775 AC XY: 57526 AN XY: 74254

African (AFR) AF: 0.866 AC: 35884 AN: 41458

American (AMR) AF: 0.840 AC: 12853 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 2366 AN: 3466

East Asian (EAS) AF: 0.764 AC: 3931 AN: 5142

South Asian (SAS) AF: 0.752 AC: 3615 AN: 4804

European-Finnish (FIN) AF: 0.706 AC: 7440 AN: 10534

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49241 AN: 67944

Other (OTH) AF: 0.782 AC: 1653 AN: 2114

Alfa AF: 0.743 Hom.: 69767

Bravo AF: 0.790

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.46
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs8057431; hg19: chr16-84839954;