chr13-85038253-C-T

Variant names:

• chr13-85038253-C-T
• rs9319110

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;