XM_011515402.4:c.1264-26451C>A

Variant names:

• chr7-15185914-G-T
• rs6962150
• XM_011515402.4:c.1264-26451C>A

Variant summary

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

The XM_011515402.4(AGMO):​c.1264-26451C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,054 control chromosomes in the GnomAD database, including 3,884 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 0.22 (3884 hom., cov: 33)
• Consequence: AGMO XM_011515402.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 3 publications found

Genes affected

AGMO (HGNC:33784): (alkylglycerol monooxygenase) The protein encoded by this gene is a tetrahydrobiopterin- and iron-dependent enzyme that cleaves the ether bond of alkylglycerols. Sequence comparisons distinguish this protein as forming a third, distinct class of tetrahydrobiopterin-dependent enzymes. Variations in this gene have been associated with decreased glucose-stimulated insulin response, type 2 diabetes, and susceptibility to intracranial aneurysms. [provided by RefSeq, Aug 2012]

AGMO Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33328 AN: 151936 Hom.: 3881 Cov.: 33

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.219 AC: 33353 AN: 152054 Hom.: 3884 Cov.: 33 AF XY: 0.222 AC XY: 16530 AN XY: 74334

African (AFR) AF: 0.284 AC: 11787 AN: 41474

American (AMR) AF: 0.243 AC: 3720 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 997 AN: 3464

East Asian (EAS) AF: 0.125 AC: 644 AN: 5164

South Asian (SAS) AF: 0.320 AC: 1543 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1828 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12200 AN: 67950

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.198 Hom.: 10313

Bravo AF: 0.223

Asia WGS AF: 0.241 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.55
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs6962150; hg19: chr7-15225539;