rs4783018

Variant names:

• chr16-82450104-G-A
• rs4783018

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 0.0696 in 152,238 control chromosomes in the GnomAD database, including 568 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 0.070 (568 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.674
• Publications: 0 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 = 0.151 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: 0.0695 AC: 10576 AN: 152120 Hom.: 564 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0627

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0706

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0255

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0696 AC: 10600 AN: 152238 Hom.: 568 Cov.: 33 AF XY: 0.0722 AC XY: 5371 AN XY: 74438

African (AFR) AF: 0.131 AC: 5458 AN: 41528

American (AMR) AF: 0.0627 AC: 959 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3470

East Asian (EAS) AF: 0.160 AC: 830 AN: 5172

South Asian (SAS) AF: 0.117 AC: 565 AN: 4820

European-Finnish (FIN) AF: 0.0706 AC: 749 AN: 10606

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0255 AC: 1734 AN: 68026

Other (OTH) AF: 0.0610 AC: 129 AN: 2114

Alfa AF: 0.0582 Hom.: 61

Bravo AF: 0.0707

Asia WGS AF: 0.147 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.23
DANN	Benign	0.55
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4783018; hg19: chr16-82483709;