rs13043313

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;