Variant rs3758149 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.239C>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 0.242 in 173,154 control chromosomes in the GnomAD database, including 5,249 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 0.24 ( 4751 hom., cov: 33)

Exomes 𝑓: 0.22 ( 498 hom. )

Consequence

GGH
ENST00000677327.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.450

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=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.287 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
GGH	ENST00000677327.1 linkuse as main transcript	n.239C>T		non_coding_transcript_exon_variant	1/8
GGH	ENST00000679326.1 linkuse as main transcript	c.-401C>T		5_prime_UTR_variant, NMD_transcript_variant	1/10

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37235

AN:

152038

Hom.:

4743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.279

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.220

AC:

4613

AN:

20998

Hom.:

498

Cov.:

AF XY:

0.217

AC XY:

2330

AN XY:

10744

show subpopulations

Gnomad4 AFR exome

AF:

0.127

Gnomad4 AMR exome

AF:

0.180

Gnomad4 ASJ exome

AF:

0.229

Gnomad4 EAS exome

AF:

0.192

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.223

Gnomad4 NFE exome

AF:

0.229

Gnomad4 OTH exome

AF:

0.230

GnomAD4 genome

AF:

0.245

AC:

37270

AN:

152156

Hom.:

4751

Cov.:

AF XY:

0.245

AC XY:

18242

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.235

Gnomad4 ASJ

AF:

0.279

Gnomad4 EAS

AF:

0.203

Gnomad4 SAS

AF:

0.300

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.282

Gnomad4 OTH

AF:

0.269

Alfa

AF:

0.254

Hom.:

597

Bravo

AF:

0.242

Asia WGS

AF:

0.260

AC:

905

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

5.1

DANN

Benign

0.91

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