13-47672039-A-G

Variant names:

• chr13-47672039-A-G
• rs10507559

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;