13-93084596-C-T

Position:

• chr13-93084596-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 0.495 in 152,028 control chromosomes in the GnomAD database, including 19,858 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 0.50 (19858 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 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: 0.495 AC: 75245 AN: 151910 Hom.: 19848 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.495 AC: 75285 AN: 152028 Hom.: 19858 Cov.: 32 AF XY: 0.501 AC XY: 37239 AN XY: 74302

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.541

Alfa AF: 0.509 Hom.: 5162

Bravo AF: 0.488

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.059
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959898; hg19: chr13-93736849;