rs13039328

Variant names:

• chr20-18499142-C-T
• rs13039328

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 0.383 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.220 AC: 9128 AN: 41470

American (AMR) AF: 0.362 AC: 5530 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2084 AN: 5162

South Asian (SAS) AF: 0.457 AC: 2203 AN: 4818

European-Finnish (FIN) AF: 0.502 AC: 5271 AN: 10510

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31575 AN: 67950

Other (OTH) AF: 0.352 AC: 744 AN: 2112

Alfa AF: 0.419 Hom.: 5504

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs13039328; hg19: chr20-18479786;