rs853858

Variant names:

• chr20-32814411-G-A
• rs853858

Your query was ambiguous. Multiple possible variants found:

• chr20-32814411-G-A
• chr20-32814411-G-T

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 0.478 in 152,126 control chromosomes in the GnomAD database, including 18,199 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 0.48 (18199 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 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: 0.478 AC: 72623 AN: 152008 Hom.: 18176 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.478 AC: 72697 AN: 152126 Hom.: 18199 Cov.: 33 AF XY: 0.475 AC XY: 35290 AN XY: 74352

African (AFR) AF: 0.626 AC: 25998 AN: 41502

American (AMR) AF: 0.461 AC: 7046 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1339 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3284 AN: 5168

South Asian (SAS) AF: 0.449 AC: 2164 AN: 4822

European-Finnish (FIN) AF: 0.394 AC: 4168 AN: 10572

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.402 AC: 27314 AN: 67980

Other (OTH) AF: 0.447 AC: 946 AN: 2116

Alfa AF: 0.419 Hom.: 14171

Bravo AF: 0.491

Asia WGS AF: 0.613 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.59
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs853858; hg19: chr20-31402217;