rs13039328

Positions:

• chr20-18499142-C-T

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 0.383 in 151,962 control chromosomes in the GnomAD database, including 12,104 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 0.38 (12104 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58245 AN: 151844 Hom.: 12108 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.383 AC: 58252 AN: 151962 Hom.: 12104 Cov.: 32 AF XY: 0.386 AC XY: 28661 AN XY: 74246

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.352

Alfa AF: 0.424 Hom.: 4419

Bravo AF: 0.362

Asia WGS AF: 0.405 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13039328; hg19: chr20-18479786;