11-117120135-A-G

Variant names:

• chr11-117120135-A-G
• rs12366015

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 0.702 in 151,502 control chromosomes in the GnomAD database, including 38,086 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 0.70 (38086 hom., cov: 30)
• Consequence: LOC101060089 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 6 publications found

Genes affected

LOC101060089 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750474.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000224077	ENST00000750474.1		n.636-3872A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106372 AN: 151382 Hom.: 38078 Cov.: 30

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.867

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.702 AC: 106407 AN: 151502 Hom.: 38086 Cov.: 30 AF XY: 0.694 AC XY: 51365 AN XY: 74064

African (AFR) AF: 0.652 AC: 26949 AN: 41306

American (AMR) AF: 0.610 AC: 9267 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2492 AN: 3462

East Asian (EAS) AF: 0.430 AC: 2197 AN: 5110

South Asian (SAS) AF: 0.530 AC: 2545 AN: 4806

European-Finnish (FIN) AF: 0.708 AC: 7458 AN: 10528

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53055 AN: 67780

Other (OTH) AF: 0.694 AC: 1461 AN: 2106

Alfa AF: 0.736 Hom.: 5147

Bravo AF: 0.694

Asia WGS AF: 0.486 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs12366015; hg19: chr11-116990851;