rs11574143

Variant names:

• chr12-47841134-C-T
• rs11574143

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 0.112 in 152,230 control chromosomes in the GnomAD database, including 1,050 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 0.11 (1050 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 36 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.112 AC: 17013 AN: 152112 Hom.: 1050 Cov.: 33

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0765

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0990

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.112 AC: 17021 AN: 152230 Hom.: 1050 Cov.: 33 AF XY: 0.117 AC XY: 8719 AN XY: 74420

African (AFR) AF: 0.0835 AC: 3472 AN: 41556

American (AMR) AF: 0.150 AC: 2293 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1118 AN: 5176

South Asian (SAS) AF: 0.0761 AC: 367 AN: 4822

European-Finnish (FIN) AF: 0.195 AC: 2064 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6735 AN: 68018

Other (OTH) AF: 0.114 AC: 241 AN: 2110

Alfa AF: 0.101 Hom.: 1656

Bravo AF: 0.111

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.80
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11574143; hg19: chr12-48234917;