rs11116589

Variant names:

• chr12-84758522-G-A
• rs11116589

Your query was ambiguous. Multiple possible variants found:

• chr12-84758522-G-A
• chr12-84758522-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.32 in 151,794 control chromosomes in the GnomAD database, including 9,778 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 0.32 (9778 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48523 AN: 151676 Hom.: 9743 Cov.: 31

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.320 AC: 48612 AN: 151794 Hom.: 9778 Cov.: 31 AF XY: 0.315 AC XY: 23352 AN XY: 74152

African (AFR) AF: 0.571 AC: 23626 AN: 41372

American (AMR) AF: 0.198 AC: 3019 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1658 AN: 5120

South Asian (SAS) AF: 0.331 AC: 1592 AN: 4810

European-Finnish (FIN) AF: 0.170 AC: 1794 AN: 10544

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15589 AN: 67924

Other (OTH) AF: 0.276 AC: 580 AN: 2098

Alfa AF: 0.256 Hom.: 23666

Bravo AF: 0.329

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11116589; hg19: chr12-85152301;