rs4783722

Variant names:

• chr16-69548009-T-C
• rs4783722

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 0.361 in 152,074 control chromosomes in the GnomAD database, including 10,341 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 0.36 (10341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.361 AC: 54847 AN: 151956 Hom.: 10344 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.361 AC: 54868 AN: 152074 Hom.: 10341 Cov.: 32 AF XY: 0.359 AC XY: 26722 AN XY: 74336

African (AFR) AF: 0.283 AC: 11751 AN: 41516

American (AMR) AF: 0.353 AC: 5386 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1580 AN: 3468

East Asian (EAS) AF: 0.114 AC: 592 AN: 5188

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4818

European-Finnish (FIN) AF: 0.427 AC: 4498 AN: 10536

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28356 AN: 67958

Other (OTH) AF: 0.357 AC: 755 AN: 2114

Alfa AF: 0.383 Hom.: 1851

Bravo AF: 0.350

Asia WGS AF: 0.259 AC: 907 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	3.6
DANN	Benign	0.50
PhyloP100		-0.086

Splicing

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

Other links and lift over

dbSNP: rs4783722; hg19: chr16-69581912;