chr13-105812808-C-T

Position:

• chr13-105812808-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 0.103 in 152,106 control chromosomes in the GnomAD database, including 993 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 0.10 (993 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.351

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.195 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: 0.103 AC: 15607 AN: 151988 Hom.: 983 Cov.: 33

Gnomad AFR AF: 0.0668

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.0859

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.0964

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.103 AC: 15647 AN: 152106 Hom.: 993 Cov.: 33 AF XY: 0.104 AC XY: 7729 AN XY: 74366

Gnomad4 AFR AF: 0.0671

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.0859

Gnomad4 NFE AF: 0.0964

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0270 Hom.: 16

Bravo AF: 0.110

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927571; hg19: chr13-106465157;