dbSNP rs719236: GGH:n.216C>A (chr8-63039192-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000679326.1(GGH):n.-424C>A 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 0.105 in 165,152 control chromosomes in the GnomAD database, including 1,044 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 0.11 ( 970 hom., cov: 33)

Exomes 𝑓: 0.10 ( 74 hom. )

Consequence

GGH
ENST00000679326.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225

Publications

4 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]

GGH links:

Genome browser will be placed here

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=-0.73).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000679326.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
GGH	ENST00000677327.1	n.216C>A	non_coding_transcript_exon	Exon 1 of 8
GGH	ENST00000679326.1	n.-424C>A	non_coding_transcript_exon	Exon 1 of 10	ENSP00000504262.1
GGH	ENST00000679326.1	n.-424C>A	5_prime_UTR	Exon 1 of 10	ENSP00000504262.1

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16072

AN:

152158

Hom.:

970

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0895

Gnomad AMI

AF:

0.0461

Gnomad AMR

AF:

0.183

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.0923

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.0882

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.103

AC:

1321

AN:

12876

Hom.:

Cov.:

AF XY:

0.103

AC XY:

680

AN XY:

6580

show subpopulations

African (AFR)

AF:

0.102

AC:

AN:

610

American (AMR)

AF:

0.188

AC:

AN:

292

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

AN:

488

East Asian (EAS)

AF:

0.189

AC:

174

AN:

920

South Asian (SAS)

AF:

0.107

AC:

AN:

112

European-Finnish (FIN)

AF:

0.0800

AC:

AN:

888

Middle Eastern (MID)

AF:

0.128

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0917

AC:

791

AN:

8630

Other (OTH)

AF:

0.104

AC:

AN:

858

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

117

175

234

292

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.106

AC:

16076

AN:

152276

Hom.:

970

Cov.:

AF XY:

0.109

AC XY:

8117

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0894

AC:

3715

AN:

41566

American (AMR)

AF:

0.183

AC:

2799

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

411

AN:

3470

East Asian (EAS)

AF:

0.214

AC:

1105

AN:

5166

South Asian (SAS)

AF:

0.0928

AC:

447

AN:

4816

European-Finnish (FIN)

AF:

0.116

AC:

1230

AN:

10614

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0883

AC:

6003

AN:

68020

Other (OTH)

AF:

0.130

AC:

276

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

720

1440

2161

2881

3601

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.0921

Hom.:

Bravo

AF:

0.113

Asia WGS

AF:

0.157

AC:

543

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

2.5

(source)

DANN

Benign

0.47

PhyloP100

-0.23

PromoterAI

0.0031

Neutral

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over