chr11-62626460-T-C

Variant names:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_198334.3(GANAB):c.2512-13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000127 in 1,580,384 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000072 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0000063 ( 0 hom. )

Consequence

GANAB
NM_198334.3 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0450

Publications

0 publications found

Variant links:

Genes affected

GANAB (HGNC:4138): (glucosidase II alpha subunit) This gene encodes the alpha subunit of glucosidase II and a member of the glycosyl hydrolase 31 family of proteins. The heterodimeric enzyme glucosidase II plays a role in protein folding and quality control by cleaving glucose residues from immature glycoproteins in the endoplasmic reticulum. Expression of the encoded protein is elevated in lung tumor tissue and in response to UV irradiation. Mutations in this gene cause autosomal-dominant polycystic kidney and liver disease. [provided by RefSeq, Jul 2016]

GANAB Gene-Disease associations (from GenCC):

polycystic kidney disease 3 with or without polycystic liver disease
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
autosomal dominant polycystic kidney disease
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

GANAB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 11-62626460-T-C is Benign according to our data. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-62626460-T-C is described in CliVar as Likely_benign. Clinvar id is 1644852.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 11 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GANAB	NM_198334.3 link	c.2512-13A>G		intron_variant	Intron 21 of 23	ENST00000356638.8	NP_938148.1	Q14697-1V9HWJ0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GANAB	ENST00000356638.8 link	c.2512-13A>G		intron_variant	Intron 21 of 23	1	NM_198334.3	ENSP00000349053.3		Q14697-1

Frequencies

GnomAD3 genomes

AF:

0.0000461

AC:

AN:

151970

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.0000199

AC:

AN:

251412

AF XY:

0.0000221

show subpopulations

Gnomad AFR exome

AF:

0.000123

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000879

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.00000630

AC:

AN:

1428296

Hom.:

Cov.:

AF XY:

0.00000702

AC XY:

AN XY:

712454

show subpopulations

African (AFR)

AF:

0.000214

AC:

AN:

32734

American (AMR)

AF:

0.00

AC:

AN:

44686

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25930

East Asian (EAS)

AF:

0.00

AC:

AN:

39550

South Asian (SAS)

AF:

0.00

AC:

AN:

85580

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53404

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5702

European-Non Finnish (NFE)

AF:

9.25e-7

AC:

AN:

1081450

Other (OTH)

AF:

0.0000169

AC:

AN:

59260

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0000723

AC:

AN:

152088

Hom.:

Cov.:

AF XY:

0.0000673

AC XY:

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.000265

AC:

AN:

41486

American (AMR)

AF:

0.00

AC:

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00

AC:

AN:

4802

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10572

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67980

Other (OTH)

AF:

0.00

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.554

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000945

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:1

Nov 29, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Polycystic kidney disease 3 with or without polycystic liver disease

Benign:1

Oct 25, 2021

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.48

PhyloP100

-0.045

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over