rs13043313

Variant names:

• chr20-62383213-T-C
• rs13043313

Your query was ambiguous. Multiple possible variants found:

• chr20-62383213-T-C
• chr20-62383213-T-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 0.271 in 152,146 control chromosomes in the GnomAD database, including 5,744 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 0.27 (5744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.912

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 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: 0.271 AC: 41135 AN: 152026 Hom.: 5740 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.271 AC: 41157 AN: 152146 Hom.: 5744 Cov.: 32 AF XY: 0.272 AC XY: 20248 AN XY: 74388

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.256

Alfa AF: 0.248 Hom.: 2068

Bravo AF: 0.267

Asia WGS AF: 0.262 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13043313; hg19: chr20-60958269;