rs4721415

Variant names:

• chr7-15196507-G-A
• rs4721415
• XM_011515402.4:c.1264-37044C>T

Variant summary

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

The XM_011515402.4(AGMO):​c.1264-37044C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,138 control chromosomes in the GnomAD database, including 1,447 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 0.13 (1447 hom., cov: 32)
• Consequence: AGMO XM_011515402.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.278
• Publications: 6 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGMO	XM_011515402.4	c.1264-37044C>T		intron_variant	Intron 12 of 12		XP_011513704.1
AGMO	XM_017012204.2	c.1264-38140C>T		intron_variant	Intron 12 of 12		XP_016867693.1
AGMO	XR_001744759.1	n.1434-38140C>T		intron_variant	Intron 12 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19463 AN: 152016 Hom.: 1441 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.0957

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.128 AC: 19497 AN: 152138 Hom.: 1447 Cov.: 32 AF XY: 0.133 AC XY: 9898 AN XY: 74366

African (AFR) AF: 0.159 AC: 6602 AN: 41468

American (AMR) AF: 0.187 AC: 2867 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3472

East Asian (EAS) AF: 0.110 AC: 568 AN: 5176

South Asian (SAS) AF: 0.266 AC: 1279 AN: 4808

European-Finnish (FIN) AF: 0.0799 AC: 846 AN: 10588

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0957 AC: 6511 AN: 68012

Other (OTH) AF: 0.115 AC: 243 AN: 2114

Alfa AF: 0.114 Hom.: 681

Bravo AF: 0.132

Asia WGS AF: 0.197 AC: 688 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.49
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4721415; hg19: chr7-15236132;