chr13-85038253-C-T

Position:

• chr13-85038253-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 0.334 in 151,864 control chromosomes in the GnomAD database, including 8,834 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 (8834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 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: 0.334 AC: 50678 AN: 151746 Hom.: 8822 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.334 AC: 50726 AN: 151864 Hom.: 8834 Cov.: 32 AF XY: 0.329 AC XY: 24405 AN XY: 74214

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.320

Alfa AF: 0.334 Hom.: 5082

Bravo AF: 0.331

Asia WGS AF: 0.232 AC: 804 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.24
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9319110; hg19: chr13-85612388;