20-20833489-G-A

Variant names:

• chr20-20833489-G-A
• rs1555901

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 0.537 in 152,024 control chromosomes in the GnomAD database, including 22,368 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 0.54 (22368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81600 AN: 151906 Hom.: 22335 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.537 AC: 81682 AN: 152024 Hom.: 22368 Cov.: 32 AF XY: 0.539 AC XY: 40085 AN XY: 74312

African (AFR) AF: 0.480 AC: 19924 AN: 41482

American (AMR) AF: 0.457 AC: 6985 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1962 AN: 3470

East Asian (EAS) AF: 0.629 AC: 3240 AN: 5154

South Asian (SAS) AF: 0.662 AC: 3192 AN: 4820

European-Finnish (FIN) AF: 0.593 AC: 6260 AN: 10564

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.564 AC: 38308 AN: 67952

Other (OTH) AF: 0.531 AC: 1122 AN: 2114

Alfa AF: 0.548 Hom.: 38363

Bravo AF: 0.518

Asia WGS AF: 0.615 AC: 2141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.36
DANN	Benign	0.80
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1555901; hg19: chr20-20814132;