13-113121768-C-T

Variant names:

• chr13-113121768-C-T
• rs3093261

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 0.299 in 152,208 control chromosomes in the GnomAD database, including 8,408 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 0.30 (8408 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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 (NFE) allele frequency at 95% confidence interval = 0.417 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: 0.299 AC: 45490 AN: 152090 Hom.: 8417 Cov.: 35

Gnomad AFR AF: 0.0984

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.299 AC: 45473 AN: 152208 Hom.: 8408 Cov.: 35 AF XY: 0.295 AC XY: 21980 AN XY: 74416

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.297

Alfa AF: 0.368 Hom.: 10567

Bravo AF: 0.278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
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: rs3093261; hg19: chr13-113776082;