dbSNP rs719235: GGH:n.286G>T (chr8-63039122-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

24 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=-0.76).

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
GGH	ENST00000677327.1 link	n.286G>T	non_coding_transcript_exon_variant	Exon 1 of 8
GGH	ENST00000679326.1 link	n.-354G>T	non_coding_transcript_exon_variant	Exon 1 of 10	ENSP00000504262.1	A0A7I2YQQ3
GGH	ENST00000679326.1 link	n.-354G>T	5_prime_UTR_variant	Exon 1 of 10	ENSP00000504262.1	A0A7I2YQQ3

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

African (AFR)

AF:

0.0505

AC:

103

AN:

2038

American (AMR)

AF:

0.198

AC:

292

AN:

1474

Ashkenazi Jewish (ASJ)

AF:

0.211

AC:

467

AN:

2212

East Asian (EAS)

AF:

0.113

AC:

540

AN:

4790

South Asian (SAS)

AF:

0.397

AC:

227

AN:

572

European-Finnish (FIN)

AF:

0.364

AC:

1451

AN:

3986

Middle Eastern (MID)

AF:

0.266

AC:

AN:

304

European-Non Finnish (NFE)

AF:

0.303

AC:

10832

AN:

35740

Other (OTH)

AF:

0.261

AC:

1012

AN:

3876

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.516

Heterozygous variant carriers

546

1092

1639

2185

2731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

112

168

224

280

<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:

0.213

AC:

32489

AN:

152180

Hom.:

4389

Cov.:

AF XY:

0.216

AC XY:

16056

AN XY:

74394

show subpopulations

African (AFR)

AF:

0.0555

AC:

2309

AN:

41580

American (AMR)

AF:

0.190

AC:

2913

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.212

AC:

737

AN:

3472

East Asian (EAS)

AF:

0.121

AC:

624

AN:

5148

South Asian (SAS)

AF:

0.351

AC:

1692

AN:

4826

European-Finnish (FIN)

AF:

0.345

AC:

3658

AN:

10590

Middle Eastern (MID)

AF:

0.245

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.292

AC:

19827

AN:

67944

Other (OTH)

AF:

0.220

AC:

465

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1206

2412

3619

4825

6031

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.249

Hom.:

8522

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

(source)

DANN

Benign

0.54

PhyloP100

-0.15

PromoterAI

0.028

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over