20-48461279-T-C

Variant names:

• chr20-48461279-T-C
• rs4402823

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 0.34 in 151,714 control chromosomes in the GnomAD database, including 9,106 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 0.34 (9106 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.340 AC: 51472 AN: 151596 Hom.: 9085 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.340 AC: 51539 AN: 151714 Hom.: 9106 Cov.: 32 AF XY: 0.348 AC XY: 25806 AN XY: 74092

African (AFR) AF: 0.347 AC: 14334 AN: 41354

American (AMR) AF: 0.467 AC: 7113 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3466

East Asian (EAS) AF: 0.522 AC: 2663 AN: 5106

South Asian (SAS) AF: 0.363 AC: 1743 AN: 4808

European-Finnish (FIN) AF: 0.366 AC: 3850 AN: 10510

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.292 AC: 19817 AN: 67938

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.325 Hom.: 1032

Bravo AF: 0.351

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs4402823; hg19: chr20-47089525;