rs13036802

Variant names:

• chr20-152134-T-C
• rs13036802

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 0.288 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.107 AC: 4445 AN: 41424

American (AMR) AF: 0.344 AC: 5257 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1546 AN: 3468

East Asian (EAS) AF: 0.228 AC: 1172 AN: 5148

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4816

European-Finnish (FIN) AF: 0.350 AC: 3677 AN: 10510

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.366 AC: 24889 AN: 67916

Other (OTH) AF: 0.303 AC: 639 AN: 2108

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs13036802; hg19: chr20-132775;