rs4815682

Variant names:

• chr20-4278466-G-A
• rs4815682

Your query was ambiguous. Multiple possible variants found:

• chr20-4278466-G-A
• chr20-4278466-G-C
• chr20-4278466-G-T

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 0.44 in 151,896 control chromosomes in the GnomAD database, including 15,432 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 0.44 (15432 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.440 AC: 66716 AN: 151778 Hom.: 15420 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.440 AC: 66766 AN: 151896 Hom.: 15432 Cov.: 31 AF XY: 0.444 AC XY: 32928 AN XY: 74242

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.454

Alfa AF: 0.426 Hom.: 7900

Bravo AF: 0.443

Asia WGS AF: 0.601 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4815682; hg19: chr20-4259113;