rs11574143

chr12-47841134-C-T

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 0.112 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.112 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

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.0761

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.0990

Gnomad4 OTH AF: 0.114

Alfa AF: 0.102 Hom.: 1234

Bravo AF: 0.111

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.2
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11574143; hg19: chr12-48234917;