11-133895472-T-C

Variant names:

• chr11-133895472-T-C
• rs329648

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 0.556 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
• Publications: 43 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 (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.310 AC: 12875 AN: 41470

American (AMR) AF: 0.491 AC: 7502 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.689 AC: 3557 AN: 5166

South Asian (SAS) AF: 0.601 AC: 2897 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8669 AN: 10600

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45065 AN: 67984

Other (OTH) AF: 0.539 AC: 1140 AN: 2116

Alfa AF: 0.630 Hom.: 55360

Bravo AF: 0.521

Asia WGS AF: 0.593 AC: 2062 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	2.4
DANN	Benign	0.50
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs329648; hg19: chr11-133765367;