rs4811719

Variant names:

• chr20-56603025-G-A
• rs4811719

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.381 in 151,868 control chromosomes in the GnomAD database, including 13,788 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 0.38 (13788 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 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: 0.381 AC: 57741 AN: 151750 Hom.: 13749 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.381 AC: 57830 AN: 151868 Hom.: 13788 Cov.: 31 AF XY: 0.378 AC XY: 28046 AN XY: 74226

African (AFR) AF: 0.683 AC: 28297 AN: 41406

American (AMR) AF: 0.293 AC: 4456 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 930 AN: 3460

East Asian (EAS) AF: 0.425 AC: 2187 AN: 5148

South Asian (SAS) AF: 0.211 AC: 1015 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2978 AN: 10548

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16999 AN: 67954

Other (OTH) AF: 0.329 AC: 695 AN: 2110

Alfa AF: 0.296 Hom.: 11727

Bravo AF: 0.398

Asia WGS AF: 0.273 AC: 952 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	0.25
DANN	Benign	0.87
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4811719; hg19: chr20-55178081;