rs4814019

Positions:

• chr20-11528332-A-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;