rs12805061

Variant names:

• chr11-116682308-A-G
• rs12805061

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;