11-134937903-C-T

Variant names:

• chr11-134937903-C-T
• rs1824832

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 0.0634 in 152,226 control chromosomes in the GnomAD database, including 384 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 0.063 (384 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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 (NFE) allele frequency at 95% confidence interval = 0.0926 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: 0.0634 AC: 9651 AN: 152108 Hom.: 383 Cov.: 32

Gnomad AFR AF: 0.0209

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0480

Gnomad FIN AF: 0.0923

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0634 AC: 9651 AN: 152226 Hom.: 384 Cov.: 32 AF XY: 0.0620 AC XY: 4613 AN XY: 74428

Gnomad4 AFR AF: 0.0208

Gnomad4 AMR AF: 0.0501

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.0923

Gnomad4 NFE AF: 0.0946

Gnomad4 OTH AF: 0.0559

Alfa AF: 0.0486 Hom.: 64

Bravo AF: 0.0569

Asia WGS AF: 0.0240 AC: 85 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	0.53
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1824832; hg19: chr11-134807797;