20-46004472-C-T

Variant names:

• chr20-46004472-C-T
• rs13040272

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 0.533 in 151,970 control chromosomes in the GnomAD database, including 22,548 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 0.53 (22548 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 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: 0.533 AC: 80899 AN: 151852 Hom.: 22545 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.533 AC: 80925 AN: 151970 Hom.: 22548 Cov.: 31 AF XY: 0.523 AC XY: 38813 AN XY: 74264

African (AFR) AF: 0.505 AC: 20897 AN: 41408

American (AMR) AF: 0.535 AC: 8165 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1958 AN: 3472

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5172

South Asian (SAS) AF: 0.398 AC: 1918 AN: 4814

European-Finnish (FIN) AF: 0.501 AC: 5289 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40604 AN: 67964

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

Alfa AF: 0.562 Hom.: 10337

Bravo AF: 0.529

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.53
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs13040272; hg19: chr20-44633111;