13-105944370-C-T

Position:

• chr13-105944370-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 0.698 in 152,004 control chromosomes in the GnomAD database, including 37,482 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 0.70 (37482 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.281

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 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: 0.698 AC: 105990 AN: 151886 Hom.: 37454 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.698 AC: 106065 AN: 152004 Hom.: 37482 Cov.: 31 AF XY: 0.700 AC XY: 51982 AN XY: 74292

Gnomad4 AFR AF: 0.633

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.848

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.744

Alfa AF: 0.715 Hom.: 29913

Bravo AF: 0.707

Asia WGS AF: 0.804 AC: 2796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488248; hg19: chr13-106596719;