chr20-4466836-A-C

Variant names:

• chr20-4466836-A-C
• rs1031825

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 0.625 in 151,228 control chromosomes in the GnomAD database, including 30,739 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 0.63 (30739 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 19 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 (NFE) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94493 AN: 151110 Hom.: 30721 Cov.: 31

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.625 AC: 94560 AN: 151228 Hom.: 30739 Cov.: 31 AF XY: 0.627 AC XY: 46332 AN XY: 73924

African (AFR) AF: 0.466 AC: 19004 AN: 40756

American (AMR) AF: 0.700 AC: 10667 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2634 AN: 5164

South Asian (SAS) AF: 0.558 AC: 2672 AN: 4792

European-Finnish (FIN) AF: 0.713 AC: 7536 AN: 10566

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47681 AN: 67936

Other (OTH) AF: 0.636 AC: 1338 AN: 2104

Alfa AF: 0.560 Hom.: 5197

Bravo AF: 0.619

Asia WGS AF: 0.561 AC: 1951 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.68
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1031825; hg19: chr20-4447483;