rs4811895

Positions:

• chr20-57631253-G-A

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 0.366 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

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 (NFE) allele frequency at 95% confidence interval = 0.501 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: 0.366 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

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.506

Gnomad4 OTH AF: 0.393

Alfa AF: 0.477 Hom.: 23321

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4811895; hg19: chr20-56206309;