rs1287059

Variant names:

• chr20-5901916-G-A
• rs1287059

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 0.448 in 151,980 control chromosomes in the GnomAD database, including 16,285 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 0.45 (16285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.732 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: 0.448 AC: 67974 AN: 151862 Hom.: 16238 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.448 AC: 68082 AN: 151980 Hom.: 16285 Cov.: 32 AF XY: 0.451 AC XY: 33508 AN XY: 74286

African (AFR) AF: 0.594 AC: 24644 AN: 41466

American (AMR) AF: 0.422 AC: 6445 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3887 AN: 5170

South Asian (SAS) AF: 0.480 AC: 2301 AN: 4794

European-Finnish (FIN) AF: 0.396 AC: 4180 AN: 10560

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24118 AN: 67936

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.408 Hom.: 2003

Bravo AF: 0.452

Asia WGS AF: 0.631 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.64
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1287059; hg19: chr20-5882562;