GeneBe

NM_016080.4:c.406+1789G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016080.4(GLOD4):​c.406+1789G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 152,206 control chromosomes in the GnomAD database, including 734 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 0.076 ( 734 hom., cov: 32)

Consequence

GLOD4
NM_016080.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

5 publications found
Variant links:
Genes affected
GLOD4 (HGNC:14111): (glyoxalase domain containing 4) Enables cadherin binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLOD4NM_016080.4 linkc.406+1789G>A intron_variant Intron 4 of 8 ENST00000301329.11 NP_057164.3 Q9HC38-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLOD4ENST00000301329.11 linkc.406+1789G>A intron_variant Intron 4 of 8 1 NM_016080.4 ENSP00000301329.6 Q9HC38-2

Frequencies

GnomAD3 genomes
AF:
0.0761
AC:
11574
AN:
152088
Hom.:
734
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0216
Gnomad AMI
AF:
0.0450
Gnomad AMR
AF:
0.135
Gnomad ASJ
AF:
0.0346
Gnomad EAS
AF:
0.338
Gnomad SAS
AF:
0.121
Gnomad FIN
AF:
0.0647
Gnomad MID
AF:
0.0605
Gnomad NFE
AF:
0.0775
Gnomad OTH
AF:
0.0750
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0761
AC:
11579
AN:
152206
Hom.:
734
Cov.:
32
AF XY:
0.0787
AC XY:
5856
AN XY:
74420
show subpopulations
African (AFR)
AF:
0.0215
AC:
894
AN:
41554
American (AMR)
AF:
0.136
AC:
2072
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.0346
AC:
120
AN:
3472
East Asian (EAS)
AF:
0.338
AC:
1742
AN:
5156
South Asian (SAS)
AF:
0.121
AC:
582
AN:
4822
European-Finnish (FIN)
AF:
0.0647
AC:
686
AN:
10608
Middle Eastern (MID)
AF:
0.0582
AC:
17
AN:
292
European-Non Finnish (NFE)
AF:
0.0775
AC:
5267
AN:
67996
Other (OTH)
AF:
0.0747
AC:
158
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
523
1046
1569
2092
2615
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
142
284
426
568
710
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0773
Hom.:
1268
Bravo
AF:
0.0794
Asia WGS
AF:
0.203
AC:
703
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.79
DANN
Benign
0.63
PhyloP100
-1.2
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs2750007; hg19: chr17-677226; API