rs12289502

Positions:

• chr11-80688369-A-C
• chr11-80688369-A-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 0.534 in 152,040 control chromosomes in the GnomAD database, including 25,150 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 0.53 (25150 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 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: 0.534 AC: 81148 AN: 151922 Hom.: 25134 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.727

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.534 AC: 81180 AN: 152040 Hom.: 25150 Cov.: 32 AF XY: 0.538 AC XY: 40005 AN XY: 74294

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.537

Alfa AF: 0.543 Hom.: 3159

Bravo AF: 0.517

Asia WGS AF: 0.539 AC: 1872 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12289502; hg19: chr11-80399413;