chr11-62634148-C-T

Position:

• chr11-62634148-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_198334.3(GANAB):​c.561-634G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,988 control chromosomes in the GnomAD database, including 10,832 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (10832 hom., cov: 31)
• Consequence: GANAB NM_198334.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.767

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BP6: Variant 11-62634148-C-T is Benign according to our data. Variant chr11-62634148-C-T is described in ClinVar as [Benign]. Clinvar id is 1253642.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GANAB	NM_198334.3	c.561-634G>A		intron_variant		ENST00000356638.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GANAB	ENST00000356638.8	c.561-634G>A		intron_variant		1	NM_198334.3	P1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51007 AN: 151870 Hom.: 10820 Cov.: 31

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.342

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.336 AC: 51029 AN: 151988 Hom.: 10832 Cov.: 31 AF XY: 0.347 AC XY: 25800 AN XY: 74268

Gnomad4 AFR AF: 0.0796

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.343

Alfa AF: 0.403 Hom.: 19058

Bravo AF: 0.315

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 21, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	6.1
DANN	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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

Other links and lift over

dbSNP: rs11231168; hg19: chr11-62401620; COSMIC: COSV60464436; COSMIC: COSV60464436;