13-105520380-A-G

Position:

• chr13-105520380-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 0.388 in 151,854 control chromosomes in the GnomAD database, including 13,215 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 (13215 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.506 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: 0.388 AC: 58948 AN: 151736 Hom.: 13204 Cov.: 30

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.388 AC: 58980 AN: 151854 Hom.: 13215 Cov.: 30 AF XY: 0.391 AC XY: 29037 AN XY: 74220

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.392

Alfa AF: 0.437 Hom.: 2542

Bravo AF: 0.384

Asia WGS AF: 0.395 AC: 1372 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9519697; hg19: chr13-106172729;