rs4815683

Variant names:

• chr20-4280002-A-C
• rs4815683

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 0.175 in 152,168 control chromosomes in the GnomAD database, including 2,702 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 0.18 (2702 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.224 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: 0.175 AC: 26661 AN: 152050 Hom.: 2701 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.175 AC: 26669 AN: 152168 Hom.: 2702 Cov.: 32 AF XY: 0.173 AC XY: 12836 AN XY: 74406

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.184

Alfa AF: 0.217 Hom.: 4878

Bravo AF: 0.165

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.37
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815683; hg19: chr20-4260649;