20-3074867-A-G

Variant names:

• chr20-3074867-A-G
• rs4813627

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 0.511 in 151,846 control chromosomes in the GnomAD database, including 20,104 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 0.51 (20104 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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: 0.511 AC: 77570 AN: 151728 Hom.: 20098 Cov.: 30

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.511 AC: 77617 AN: 151846 Hom.: 20104 Cov.: 30 AF XY: 0.512 AC XY: 37979 AN XY: 74208

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.542

Alfa AF: 0.487 Hom.: 23974

Bravo AF: 0.512

Asia WGS AF: 0.575 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4813627; hg19: chr20-3055513;