rs12805061

Positions:

• chr11-116682308-A-G

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 0.255 in 151,872 control chromosomes in the GnomAD database, including 5,188 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 0.26 (5188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 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: 0.255 AC: 38717 AN: 151756 Hom.: 5185 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.255 AC: 38732 AN: 151872 Hom.: 5188 Cov.: 32 AF XY: 0.258 AC XY: 19120 AN XY: 74204

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.220

Alfa AF: 0.232 Hom.: 8386

Bravo AF: 0.250

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.41
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12805061; hg19: chr11-116553025;