rs4783722

Variant names:

• chr16-69548009-T-C
• rs4783722

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 0.361 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.361 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

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.114

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.357

Alfa AF: 0.386 Hom.: 1813

Bravo AF: 0.350

Asia WGS AF: 0.259 AC: 907 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4783722; hg19: chr16-69581912;