13-105346321-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 0.293 in 152,042 control chromosomes in the GnomAD database, including 7,464 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 0.29 (7464 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) 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: 0.293 AC: 44468 AN: 151926 Hom.: 7466 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.293 AC: 44473 AN: 152042 Hom.: 7464 Cov.: 32 AF XY: 0.289 AC XY: 21507 AN XY: 74314

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.0877

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.291

Alfa AF: 0.101 Hom.: 163

Bravo AF: 0.270

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.2
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs746187; hg19: chr13-105998672;