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GeneBe

rs2070600

Variant summary

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

The NM_001136.5(AGER):c.244G>A(p.Gly82Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0561 in 1,613,010 control chromosomes in the GnomAD database, including 3,365 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.039 ( 234 hom., cov: 33)
Exomes 𝑓: 0.058 ( 3131 hom. )

Consequence

AGER
NM_001136.5 missense

Scores

2
3
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.46
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 (MetaRNN=0.0016931295).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AGERNM_001136.5 linkuse as main transcriptc.244G>A p.Gly82Ser missense_variant 3/11 ENST00000375076.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGERENST00000375076.9 linkuse as main transcriptc.244G>A p.Gly82Ser missense_variant 3/111 NM_001136.5 P1Q15109-1

Frequencies

GnomAD3 genomes
AF:
0.0388
AC:
5905
AN:
152132
Hom.:
234
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00990
Gnomad AMI
AF:
0.0428
Gnomad AMR
AF:
0.00981
Gnomad ASJ
AF:
0.00980
Gnomad EAS
AF:
0.207
Gnomad SAS
AF:
0.0614
Gnomad FIN
AF:
0.0702
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0456
Gnomad OTH
AF:
0.0239
GnomAD3 exomes
AF:
0.0532
AC:
13091
AN:
245924
Hom.:
666
AF XY:
0.0540
AC XY:
7250
AN XY:
134274
show subpopulations
Gnomad AFR exome
AF:
0.00921
Gnomad AMR exome
AF:
0.00676
Gnomad ASJ exome
AF:
0.0107
Gnomad EAS exome
AF:
0.207
Gnomad SAS exome
AF:
0.0656
Gnomad FIN exome
AF:
0.0686
Gnomad NFE exome
AF:
0.0463
Gnomad OTH exome
AF:
0.0409
GnomAD4 exome
AF:
0.0580
AC:
84662
AN:
1460760
Hom.:
3131
Cov.:
36
AF XY:
0.0575
AC XY:
41809
AN XY:
726696
show subpopulations
Gnomad4 AFR exome
AF:
0.00765
Gnomad4 AMR exome
AF:
0.00738
Gnomad4 ASJ exome
AF:
0.00983
Gnomad4 EAS exome
AF:
0.174
Gnomad4 SAS exome
AF:
0.0622
Gnomad4 FIN exome
AF:
0.0647
Gnomad4 NFE exome
AF:
0.0583
Gnomad4 OTH exome
AF:
0.0539
GnomAD4 genome
AF:
0.0387
AC:
5895
AN:
152250
Hom.:
234
Cov.:
33
AF XY:
0.0403
AC XY:
3002
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.00987
Gnomad4 AMR
AF:
0.00980
Gnomad4 ASJ
AF:
0.00980
Gnomad4 EAS
AF:
0.206
Gnomad4 SAS
AF:
0.0611
Gnomad4 FIN
AF:
0.0702
Gnomad4 NFE
AF:
0.0456
Gnomad4 OTH
AF:
0.0241
Alfa
AF:
0.0477
Hom.:
565
Bravo
AF:
0.0339
TwinsUK
AF:
0.0655
AC:
243
ALSPAC
AF:
0.0804
AC:
310
ESP6500AA
AF:
0.0156
AC:
47
ESP6500EA
AF:
0.0456
AC:
247
ExAC
AF:
0.0530
AC:
6195
Asia WGS
AF:
0.104
AC:
361
AN:
3478
EpiCase
AF:
0.0405
EpiControl
AF:
0.0414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Benign
-0.52
T
BayesDel_noAF
Benign
-0.37
Cadd
Pathogenic
34
Dann
Uncertain
1.0
Eigen
Uncertain
0.67
Eigen_PC
Pathogenic
0.68
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.84
T;T;T;T;T;T;T;T;T
MetaRNN
Benign
0.0017
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.2
T
MutationTaster
Benign
0.0020
P;P;P;P;P;P;P;P;P
PrimateAI
Benign
0.46
T
PROVEAN
Benign
-1.9
N;N;N;.;.;N;N;N;D
REVEL
Benign
0.16
Sift
Benign
0.51
T;T;T;.;.;T;T;T;D
Sift4G
Pathogenic
0.0
D;D;D;D;D;D;.;.;D
Polyphen
1.0
D;D;.;.;.;D;.;.;.
Vest4
0.69
MPC
0.65
ClinPred
0.040
T
GERP RS
5.8
Varity_R
0.20
gMVP
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.73
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.73
Position offset: -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: rs2070600; hg19: chr6-32151443; API