Variant 8-63039122-C-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000677327.1(GGH):n.286G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 207,172 control chromosomes in the GnomAD database, including 6,592 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 0.21 ( 4389 hom., cov: 33)

Exomes 𝑓: 0.27 ( 2203 hom. )

Consequence

GGH
ENST00000677327.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.151

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]

GGH links:

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=-0.76).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GGH	ENST00000677327.1 linkuse as main transcript	n.286G>T		non_coding_transcript_exon_variant	1/8
GGH	ENST00000679326.1 linkuse as main transcript	c.-354G>T		5_prime_UTR_variant, NMD_transcript_variant	1/10			ENSP00000504262

Frequencies

GnomAD3 genomes

AF:

0.214

AC:

32479

AN:

152062

Hom.:

4382

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0557

Gnomad AMI

AF:

0.211

Gnomad AMR

AF:

0.191

Gnomad ASJ

AF:

0.212

Gnomad EAS

AF:

0.122

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.292

Gnomad OTH

AF:

0.212

GnomAD4 exome

AF:

0.273

AC:

15005

AN:

54992

Hom.:

2203

Cov.:

AF XY:

0.276

AC XY:

7657

AN XY:

27792

show subpopulations

Gnomad4 AFR exome

AF:

0.0505

Gnomad4 AMR exome

AF:

0.198

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.397

Gnomad4 FIN exome

AF:

0.364

Gnomad4 NFE exome

AF:

0.303

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.213

AC:

32489

AN:

152180

Hom.:

4389

Cov.:

AF XY:

0.216

AC XY:

16056

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0555

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.212

Gnomad4 EAS

AF:

0.121

Gnomad4 SAS

AF:

0.351

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.292

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.252

Hom.:

894

Bravo

AF:

0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.3

DANN

Benign

0.54

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over