GeneBe

ENST00000677327.1:n.-10G>A

Variant names:

Variant summary

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

The ENST00000677327.1(GGH):​n.-10G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,178 control chromosomes in the GnomAD database, including 51,478 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 0.82 ( 51478 hom., cov: 32)

Consequence

GGH
ENST00000677327.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

Publications

2 publications found
Variant links:
Genes affected
GGH (HGNC:4248): (gamma-glutamyl hydrolase) This gene catalyzes the hydrolysis of folylpoly-gamma-glutamates and antifolylpoly-gamma-glutamates by the removal of gamma-linked polyglutamates and glutamate. [provided by RefSeq, Jul 2008]

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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=-0.78).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.955 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GGHENST00000677327.1 linkn.-10G>A upstream_gene_variant
GGHENST00000679326.1 linkn.-649G>A upstream_gene_variant ENSP00000504262.1 A0A7I2YQQ3

Frequencies

GnomAD3 genomes
AF:
0.818
AC:
124323
AN:
152060
Hom.:
51411
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.927
Gnomad AMI
AF:
0.729
Gnomad AMR
AF:
0.829
Gnomad ASJ
AF:
0.756
Gnomad EAS
AF:
0.977
Gnomad SAS
AF:
0.885
Gnomad FIN
AF:
0.810
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.806
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.818
AC:
124450
AN:
152178
Hom.:
51478
Cov.:
32
AF XY:
0.824
AC XY:
61297
AN XY:
74394
show subpopulations
African (AFR)
AF:
0.927
AC:
38498
AN:
41544
American (AMR)
AF:
0.829
AC:
12676
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.756
AC:
2624
AN:
3472
East Asian (EAS)
AF:
0.977
AC:
5034
AN:
5152
South Asian (SAS)
AF:
0.886
AC:
4270
AN:
4822
European-Finnish (FIN)
AF:
0.810
AC:
8588
AN:
10602
Middle Eastern (MID)
AF:
0.755
AC:
222
AN:
294
European-Non Finnish (NFE)
AF:
0.738
AC:
50170
AN:
67984
Other (OTH)
AF:
0.809
AC:
1706
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1118
2237
3355
4474
5592
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
874
1748
2622
3496
4370
<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:
0.780
Hom.:
17026
Bravo
AF:
0.824
Asia WGS
AF:
0.924
AC:
3214
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
0.15
DANN
Benign
0.83
PhyloP100
-2.0

Splicing

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

Publications

Other links and lift over

dbSNP: rs2736676; hg19: chr8-63951976; API