rs13036802

chr20-152134-T-C

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 0.288 in 151,856 control chromosomes in the GnomAD database, including 7,349 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 0.29 (7349 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.363 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: 0.289 AC: 43789 AN: 151738 Hom.: 7354 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.288 AC: 43783 AN: 151856 Hom.: 7349 Cov.: 31 AF XY: 0.290 AC XY: 21507 AN XY: 74200

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.303

Alfa AF: 0.259 Hom.: 1175

Bravo AF: 0.280

Asia WGS AF: 0.233 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	4.0
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13036802; hg19: chr20-132775;