rs4783018

chr16-82450104-G-A

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 0.0696 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0627

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0706

Gnomad4 NFE AF: 0.0255

Gnomad4 OTH AF: 0.0610

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.23
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4783018; hg19: chr16-82483709;