chr13-81906466-A-G

Position:

• chr13-81906466-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 0.387 in 151,922 control chromosomes in the GnomAD database, including 12,069 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 0.39 (12069 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58774 AN: 151806 Hom.: 12059 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.387 AC: 58825 AN: 151922 Hom.: 12069 Cov.: 32 AF XY: 0.386 AC XY: 28647 AN XY: 74262

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.346

Alfa AF: 0.303 Hom.: 1634

Bravo AF: 0.388

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4456389; hg19: chr13-82480601;