20-43858564-C-T

Variant names:

• chr20-43858564-C-T
• rs6103489

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 0.511 in 151,960 control chromosomes in the GnomAD database, including 20,110 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 0.51 (20110 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77488 AN: 151842 Hom.: 20069 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.511 AC: 77580 AN: 151960 Hom.: 20110 Cov.: 31 AF XY: 0.516 AC XY: 38334 AN XY: 74266

African (AFR) AF: 0.580 AC: 24019 AN: 41436

American (AMR) AF: 0.532 AC: 8126 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1682 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3214 AN: 5172

South Asian (SAS) AF: 0.624 AC: 3000 AN: 4806

European-Finnish (FIN) AF: 0.444 AC: 4668 AN: 10524

Middle Eastern (MID) AF: 0.562 AC: 164 AN: 292

European-Non Finnish (NFE) AF: 0.459 AC: 31219 AN: 67962

Other (OTH) AF: 0.499 AC: 1052 AN: 2108

Alfa AF: 0.482 Hom.: 27123

Bravo AF: 0.518

Asia WGS AF: 0.582 AC: 2021 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.34
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6103489; hg19: chr20-42487204;