20-4406487-C-T

Variant names:

• chr20-4406487-C-T
• rs586446

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 0.902 in 152,214 control chromosomes in the GnomAD database, including 62,067 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 0.90 (62067 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 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: 0.902 AC: 137224 AN: 152096 Hom.: 62002 Cov.: 31

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.902 AC: 137349 AN: 152214 Hom.: 62067 Cov.: 31 AF XY: 0.905 AC XY: 67384 AN XY: 74426

African (AFR) AF: 0.946 AC: 39275 AN: 41534

American (AMR) AF: 0.879 AC: 13429 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2990 AN: 3472

East Asian (EAS) AF: 0.991 AC: 5127 AN: 5174

South Asian (SAS) AF: 0.964 AC: 4646 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9562 AN: 10608

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59414 AN: 68006

Other (OTH) AF: 0.879 AC: 1859 AN: 2114

Alfa AF: 0.905 Hom.: 20248

Bravo AF: 0.901

Asia WGS AF: 0.973 AC: 3384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.19
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs586446; hg19: chr20-4387134;