rs1413020

Variant names:

• chr20-12749395-C-G
• rs1413020

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 0.088 in 152,244 control chromosomes in the GnomAD database, including 692 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 0.088 (692 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0881 AC: 13396 AN: 152126 Hom.: 693 Cov.: 32

Gnomad AFR AF: 0.0598

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.0759

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0984

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0880 AC: 13398 AN: 152244 Hom.: 692 Cov.: 32 AF XY: 0.0877 AC XY: 6533 AN XY: 74456

African (AFR) AF: 0.0600 AC: 2493 AN: 41538

American (AMR) AF: 0.0757 AC: 1158 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3472

East Asian (EAS) AF: 0.187 AC: 966 AN: 5178

South Asian (SAS) AF: 0.160 AC: 771 AN: 4818

European-Finnish (FIN) AF: 0.0397 AC: 421 AN: 10616

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0984 AC: 6692 AN: 68006

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0870 Hom.: 81

Bravo AF: 0.0887

Asia WGS AF: 0.170 AC: 589 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1413020; hg19: chr20-12730042;