7-15218831-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.84
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
AGMONM_001004320.2 linkuse as main transcriptc.1264-17472G>A intron_variant ENST00000342526.8
AGMOXM_011515402.4 linkuse as main transcriptc.1264-59368G>A intron_variant
AGMOXM_017012204.2 linkuse as main transcriptc.1264-60464G>A intron_variant
AGMOXR_001744759.1 linkuse as main transcriptn.1434-60464G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGMOENST00000342526.8 linkuse as main transcriptc.1264-17472G>A intron_variant 1 NM_001004320.2 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6977610; hg19: chr7-15258456; API