rs2269422

Variant summary

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

The NM_001136.5(AGER):​c.355+38A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00683 in 1,612,698 control chromosomes in the GnomAD database, including 434 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 0.0077 ( 69 hom., cov: 33)
Exomes 𝑓: 0.0067 ( 365 hom. )

Consequence

AGER
NM_001136.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91
Variant links:
Genes affected
AGER (HGNC:320): (advanced glycosylation end-product specific receptor) The advanced glycosylation end product (AGE) receptor encoded by this gene is a member of the immunoglobulin superfamily of cell surface receptors. It is a multiligand receptor, and besides AGE, interacts with other molecules implicated in homeostasis, development, and inflammation, and certain diseases, such as diabetes and Alzheimer's disease. Many alternatively spliced transcript variants encoding different isoforms, as well as non-protein-coding variants, have been described for this gene (PMID:18089847). [provided by RefSeq, May 2011]

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=-0.84).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGERNM_001136.5 linkuse as main transcriptc.355+38A>G intron_variant ENST00000375076.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGERENST00000375076.9 linkuse as main transcriptc.355+38A>G intron_variant 1 NM_001136.5 P1Q15109-1

Frequencies

GnomAD3 genomes
AF:
0.00769
AC:
1170
AN:
152072
Hom.:
71
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00602
Gnomad ASJ
AF:
0.00173
Gnomad EAS
AF:
0.110
Gnomad SAS
AF:
0.0677
Gnomad FIN
AF:
0.000471
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00140
Gnomad OTH
AF:
0.00575
GnomAD3 exomes
AF:
0.0168
AC:
4131
AN:
246364
Hom.:
201
AF XY:
0.0179
AC XY:
2406
AN XY:
134276
show subpopulations
Gnomad AFR exome
AF:
0.00179
Gnomad AMR exome
AF:
0.00833
Gnomad ASJ exome
AF:
0.000702
Gnomad EAS exome
AF:
0.117
Gnomad SAS exome
AF:
0.0484
Gnomad FIN exome
AF:
0.000324
Gnomad NFE exome
AF:
0.00129
Gnomad OTH exome
AF:
0.00857
GnomAD4 exome
AF:
0.00674
AC:
9842
AN:
1460508
Hom.:
365
Cov.:
34
AF XY:
0.00802
AC XY:
5830
AN XY:
726580
show subpopulations
Gnomad4 AFR exome
AF:
0.00108
Gnomad4 AMR exome
AF:
0.00872
Gnomad4 ASJ exome
AF:
0.00111
Gnomad4 EAS exome
AF:
0.0789
Gnomad4 SAS exome
AF:
0.0492
Gnomad4 FIN exome
AF:
0.000459
Gnomad4 NFE exome
AF:
0.00102
Gnomad4 OTH exome
AF:
0.0124
GnomAD4 genome
AF:
0.00765
AC:
1165
AN:
152190
Hom.:
69
Cov.:
33
AF XY:
0.00934
AC XY:
695
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.00149
Gnomad4 AMR
AF:
0.00602
Gnomad4 ASJ
AF:
0.00173
Gnomad4 EAS
AF:
0.109
Gnomad4 SAS
AF:
0.0677
Gnomad4 FIN
AF:
0.000471
Gnomad4 NFE
AF:
0.00140
Gnomad4 OTH
AF:
0.00664
Alfa
AF:
0.00188
Hom.:
3
Bravo
AF:
0.00643
Asia WGS
AF:
0.0670
AC:
233
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
0.15
DANN
Benign
0.51

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: rs2269422; hg19: chr6-32151294; API