20-46005911-T-C

Variant names:

• chr20-46005911-T-C
• rs4810482

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 0.452 in 152,020 control chromosomes in the GnomAD database, including 16,833 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 (16833 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460
• Publications: 33 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68635 AN: 151902 Hom.: 16807 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.452 AC: 68704 AN: 152020 Hom.: 16833 Cov.: 31 AF XY: 0.456 AC XY: 33883 AN XY: 74312

African (AFR) AF: 0.629 AC: 26056 AN: 41444

American (AMR) AF: 0.304 AC: 4643 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3466

East Asian (EAS) AF: 0.724 AC: 3744 AN: 5168

South Asian (SAS) AF: 0.517 AC: 2493 AN: 4822

European-Finnish (FIN) AF: 0.429 AC: 4535 AN: 10564

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24599 AN: 67966

Other (OTH) AF: 0.404 AC: 853 AN: 2110

Alfa AF: 0.388 Hom.: 12489

Bravo AF: 0.451

Asia WGS AF: 0.570 AC: 1980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.8
DANN	Benign	0.74
PhyloP100		-0.046

Splicing

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

Other links and lift over

dbSNP: rs4810482; hg19: chr20-44634550; COSMIC: COSV64886008;