13-106403247-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.331 in 152,076 control chromosomes in the GnomAD database, including 9,059 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 0.33 (9059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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: 0.332 AC: 50399 AN: 151958 Hom.: 9064 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.331 AC: 50397 AN: 152076 Hom.: 9059 Cov.: 32 AF XY: 0.327 AC XY: 24299 AN XY: 74370

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.327

Alfa AF: 0.237 Hom.: 592

Bravo AF: 0.319

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
Cadd	Benign	19
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492641; hg19: chr13-107055595;