rs2736676

Variant summary

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

The 8-63039417-C-T 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
ENST00000679326.1 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02
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 made for transcript

Verdict is Benign. Variant got -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/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GGHENST00000677327.1 linkuse as main transcript upstream_gene_variant
GGHENST00000679326.1 linkuse as main transcript upstream_gene_variant

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
Gnomad4 AFR
AF:
0.927
Gnomad4 AMR
AF:
0.829
Gnomad4 ASJ
AF:
0.756
Gnomad4 EAS
AF:
0.977
Gnomad4 SAS
AF:
0.886
Gnomad4 FIN
AF:
0.810
Gnomad4 NFE
AF:
0.738
Gnomad4 OTH
AF:
0.809
Alfa
AF:
0.782
Hom.:
10374
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

Splicing

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: rs2736676; hg19: chr8-63951976; API