13-47672039-A-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 0.31 in 152,108 control chromosomes in the GnomAD database, including 8,932 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 0.31 (8932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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: 0.310 AC: 47169 AN: 151990 Hom.: 8931 Cov.: 32

Gnomad AFR AF: 0.0930

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.310 AC: 47178 AN: 152108 Hom.: 8932 Cov.: 32 AF XY: 0.314 AC XY: 23368 AN XY: 74342

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.333

Alfa AF: 0.366 Hom.: 5024

Bravo AF: 0.301

Asia WGS AF: 0.380 AC: 1320 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.63
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507559; hg19: chr13-48246174;