11-134937903-C-T

Variant names:

• chr11-134937903-C-T
• rs1824832

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0208 AC: 865 AN: 41560

American (AMR) AF: 0.0501 AC: 766 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3468

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5170

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4826

European-Finnish (FIN) AF: 0.0923 AC: 978 AN: 10592

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6430 AN: 68002

Other (OTH) AF: 0.0559 AC: 118 AN: 2110

Alfa AF: 0.0474 Hom.: 65

Bravo AF: 0.0569

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.53
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1824832; hg19: chr11-134807797;