chr7-15218831-C-T

Position:

• chr7-15218831-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004320.2(AGMO):​c.1264-17472G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 151,862 control chromosomes in the GnomAD database, including 4,906 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 0.24 (4906 hom., cov: 31)
• Consequence: AGMO NM_001004320.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.84

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGMO	NM_001004320.2	c.1264-17472G>A		intron_variant		ENST00000342526.8
AGMO	XM_011515402.4	c.1264-59368G>A		intron_variant
AGMO	XM_017012204.2	c.1264-60464G>A		intron_variant
AGMO	XR_001744759.1	n.1434-60464G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGMO	ENST00000342526.8	c.1264-17472G>A		intron_variant		1	NM_001004320.2	P1

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36051 AN: 151744 Hom.: 4891 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0327

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.238 AC: 36104 AN: 151862 Hom.: 4906 Cov.: 31 AF XY: 0.237 AC XY: 17591 AN XY: 74220

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0326

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.208

Alfa AF: 0.192 Hom.: 2596

Bravo AF: 0.246

Asia WGS AF: 0.220 AC: 767 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.021
DANN	Benign	0.18

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6977610; hg19: chr7-15258456;