chr11-13267151-G-T

Variant names:

• chr11-13267151-G-T
• rs7942486

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 0.481 in 152,014 control chromosomes in the GnomAD database, including 18,123 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 0.48 (18123 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 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: 0.482 AC: 73141 AN: 151896 Hom.: 18119 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.481 AC: 73176 AN: 152014 Hom.: 18123 Cov.: 32 AF XY: 0.477 AC XY: 35417 AN XY: 74282

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.502

Alfa AF: 0.543 Hom.: 25390

Bravo AF: 0.477

Asia WGS AF: 0.389 AC: 1350 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0060
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7942486; hg19: chr11-13288698;