rs1413020

chr20-12749395-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.0757

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0984

Gnomad4 OTH AF: 0.102

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1413020; hg19: chr20-12730042;