rs12575381

Positions:

• chr11-135033566-G-A

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 0.154 in 152,084 control chromosomes in the GnomAD database, including 1,931 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 0.15 (1931 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23434 AN: 151966 Hom.: 1925 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0780

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.154 AC: 23470 AN: 152084 Hom.: 1931 Cov.: 33 AF XY: 0.156 AC XY: 11562 AN XY: 74322

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.0781

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.135

Alfa AF: 0.152 Hom.: 231

Bravo AF: 0.152

Asia WGS AF: 0.156 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12575381; hg19: chr11-134903460;