chr13-104367011-C-A

Position:

• chr13-104367011-C-A

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 0.219 in 152,028 control chromosomes in the GnomAD database, including 3,953 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 0.22 (3953 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33302 AN: 151910 Hom.: 3947 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33341 AN: 152028 Hom.: 3953 Cov.: 32 AF XY: 0.223 AC XY: 16567 AN XY: 74294

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.198

Alfa AF: 0.162 Hom.: 576

Bravo AF: 0.219

Asia WGS AF: 0.306 AC: 1063 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.76
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs714668; hg19: chr13-105019361;