rs4814019

Variant names:

• chr20-11528332-A-C
• rs4814019

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 0.371 in 151,952 control chromosomes in the GnomAD database, including 10,920 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 0.37 (10920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806

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 (AFR) allele frequency at 95% confidence interval = 0.486 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: 0.371 AC: 56331 AN: 151834 Hom.: 10916 Cov.: 32

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.371 AC: 56374 AN: 151952 Hom.: 10920 Cov.: 32 AF XY: 0.372 AC XY: 27603 AN XY: 74258

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.377

Alfa AF: 0.322 Hom.: 14666

Bravo AF: 0.372

Asia WGS AF: 0.361 AC: 1252 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	1.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4814019; hg19: chr20-11508980;