11-133895472-T-C

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 0.556 in 152,122 control chromosomes in the GnomAD database, including 25,683 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 0.56 (25683 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84537 AN: 152004 Hom.: 25696 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.556 AC: 84539 AN: 152122 Hom.: 25683 Cov.: 32 AF XY: 0.562 AC XY: 41821 AN XY: 74368

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.539

Alfa AF: 0.615 Hom.: 11493

Bravo AF: 0.521

Asia WGS AF: 0.593 AC: 2062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.4
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs329648; hg19: chr11-133765367;