rs4811072

Variant names:

• chr20-50469580-G-A
• rs4811072

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 0.798 in 151,998 control chromosomes in the GnomAD database, including 49,102 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 0.80 (49102 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.911 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: 0.798 AC: 121231 AN: 151880 Hom.: 49056 Cov.: 30

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.798 AC: 121327 AN: 151998 Hom.: 49102 Cov.: 30 AF XY: 0.799 AC XY: 59358 AN XY: 74272

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.775

Alfa AF: 0.750 Hom.: 70777

Bravo AF: 0.805

Asia WGS AF: 0.712 AC: 2477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
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: rs4811072; hg19: chr20-49086117;