Variant rs11545076 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000677327.1(GGH):n.516T>G 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 0.247 in 487,604 control chromosomes in the GnomAD database, including 15,498 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 0.25 ( 4751 hom., cov: 33)

Exomes 𝑓: 0.25 ( 10747 hom. )

Consequence

GGH
ENST00000677327.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.180

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.46).

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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	Protein
GGH	ENST00000677327.1 linkuse as main transcript	n.516T>G	non_coding_transcript_exon_variant	1/8
GGH	ENST00000679326.1 linkuse as main transcript	c.-124T>G	5_prime_UTR_variant, NMD_transcript_variant	1/10	ENSP00000504262
GGH	ENST00000677482.1 linkuse as main transcript		upstream_gene_variant		ENSP00000504590

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37232

AN:

151920

Hom.:

4742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.341

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.278

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.282

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.247

AC:

83021

AN:

335572

Hom.:

10747

Cov.:

AF XY:

0.250

AC XY:

43872

AN XY:

175212

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.234

Gnomad4 ASJ exome

AF:

0.274

Gnomad4 EAS exome

AF:

0.213

Gnomad4 SAS exome

AF:

0.239

Gnomad4 FIN exome

AF:

0.243

Gnomad4 NFE exome

AF:

0.255

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.245

AC:

37265

AN:

152032

Hom.:

4751

Cov.:

AF XY:

0.245

AC XY:

18246

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.178

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.278

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.:

600

Bravo

AF:

0.242

Asia WGS

AF:

0.259

AC:

901

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Benign

0.81

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