rs4811895

Variant names:

• chr20-57631253-G-A
• rs4811895

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 0.366 in 152,062 control chromosomes in the GnomAD database, including 12,006 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 (12006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.588
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.366 AC: 55616 AN: 151944 Hom.: 12007 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.366 AC: 55609 AN: 152062 Hom.: 12006 Cov.: 32 AF XY: 0.358 AC XY: 26639 AN XY: 74326

African (AFR) AF: 0.145 AC: 6004 AN: 41492

American (AMR) AF: 0.388 AC: 5933 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1447 AN: 3468

East Asian (EAS) AF: 0.135 AC: 701 AN: 5188

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4814

European-Finnish (FIN) AF: 0.405 AC: 4266 AN: 10540

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.506 AC: 34359 AN: 67962

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.459 Hom.: 30874

Bravo AF: 0.354

Asia WGS AF: 0.230 AC: 804 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	2.0
DANN	Benign	0.53
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs4811895; hg19: chr20-56206309;