chr13-113121768-C-T

Variant names:

• chr13-113121768-C-T
• rs3093261

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0981 AC: 4076 AN: 41544

American (AMR) AF: 0.271 AC: 4142 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1274 AN: 3470

East Asian (EAS) AF: 0.125 AC: 646 AN: 5160

South Asian (SAS) AF: 0.302 AC: 1460 AN: 4828

European-Finnish (FIN) AF: 0.391 AC: 4148 AN: 10606

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28636 AN: 67988

Other (OTH) AF: 0.297 AC: 628 AN: 2114

Alfa AF: 0.354 Hom.: 14849

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs3093261; hg19: chr13-113776082;