13-106190907-C-T

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 0.572 in 151,990 control chromosomes in the GnomAD database, including 27,611 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 0.57 (27611 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

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 (NFE) allele frequency at 95% confidence interval = 0.708 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: 0.572 AC: 86886 AN: 151872 Hom.: 27610 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.572 AC: 86903 AN: 151990 Hom.: 27611 Cov.: 33 AF XY: 0.574 AC XY: 42610 AN XY: 74286

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.702

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.605

Alfa AF: 0.632 Hom.: 3986

Bravo AF: 0.550

Asia WGS AF: 0.558 AC: 1940 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	0.67
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1978945; hg19: chr13-106843256;