11-13263734-T-G

Variant names:

• chr11-13263734-T-G
• rs2403661

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 0.68 in 151,916 control chromosomes in the GnomAD database, including 35,238 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 0.68 (35238 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 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: 0.680 AC: 103205 AN: 151798 Hom.: 35196 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.680 AC: 103301 AN: 151916 Hom.: 35238 Cov.: 31 AF XY: 0.681 AC XY: 50548 AN XY: 74250

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.661

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.689

Alfa AF: 0.686 Hom.: 16937

Bravo AF: 0.676

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2403661; hg19: chr11-13285281;