chr11-134602767-T-A

Variant names:

• chr11-134602767-T-A
• rs4300405

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.841 in 152,196 control chromosomes in the GnomAD database, including 53,945 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 0.84 (53945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.857 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: 0.841 AC: 127922 AN: 152078 Hom.: 53898 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.841 AC: 128026 AN: 152196 Hom.: 53945 Cov.: 32 AF XY: 0.842 AC XY: 62677 AN XY: 74416

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.846

Alfa AF: 0.855 Hom.: 6907

Bravo AF: 0.835

Asia WGS AF: 0.784 AC: 2726 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	12
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4300405; hg19: chr11-134472661;