Variant 16-88856712-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000512.5(GALNS):c.120+46A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.035 ( 98 hom., cov: 20)

Exomes 𝑓: 0.035 ( 168 hom. )

Consequence

GALNS
NM_000512.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.348

Variant links:

Genes affected

GALNS (HGNC:4122): (galactosamine (N-acetyl)-6-sulfatase) This gene encodes N-acetylgalactosamine-6-sulfatase which is a lysosomal exohydrolase required for the degradation of the glycosaminoglycans, keratan sulfate, and chondroitin 6-sulfate. Sequence alterations including point, missense and nonsense mutations, as well as those that affect splicing, result in a deficiency of this enzyme. Deficiencies of this enzyme lead to Morquio A syndrome, a lysosomal storage disorder. [provided by RefSeq, Jul 2008]

GALNS links:

TRAPPC2L (HGNC:30887): (trafficking protein particle complex subunit 2L) This gene encodes a protein that interacts with the tethering factor trafficking protein particle (TRAPP complex). TRAPP complexes mediate the contact between vescicles and target membranes, and thus, are involved in vescicle-mediated transport of proteins and lipids. The encoded protein is related to the X-linked trafficking protein particle complex 2. A related pseudogene is located on the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

TRAPPC2L links:

GALNS (HGNC:):

GALNS links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 16-88856712-T-G is Benign according to our data. Variant chr16-88856712-T-G is described in ClinVar as [Benign]. Clinvar id is 1289536.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GALNS	NM_000512.5 linkuse as main transcript	c.120+46A>C		intron_variant		ENST00000268695.10	NP_000503.1	P34059Q96I49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GALNS	ENST00000268695.10 linkuse as main transcript	c.120+46A>C		intron_variant		1	NM_000512.5	ENSP00000268695.5		P34059

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

4449

AN:

127420

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0562

Gnomad AMI

AF:

0.0174

Gnomad AMR

AF:

0.0263

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.0220

Gnomad SAS

AF:

0.0143

Gnomad FIN

AF:

0.0409

Gnomad MID

AF:

0.0106

Gnomad NFE

AF:

0.0275

Gnomad OTH

AF:

0.0356

GnomAD3 exomes

AF:

0.0304

AC:

1357

AN:

44702

Hom.:

AF XY:

0.0302

AC XY:

706

AN XY:

23406

show subpopulations

Gnomad AFR exome

AF:

0.0584

Gnomad AMR exome

AF:

0.0244

Gnomad ASJ exome

AF:

0.0184

Gnomad EAS exome

AF:

0.0265

Gnomad SAS exome

AF:

0.0163

Gnomad FIN exome

AF:

0.0408

Gnomad NFE exome

AF:

0.0324

Gnomad OTH exome

AF:

0.0308

GnomAD4 exome

AF:

0.0346

AC:

10393

AN:

300556

Hom.:

168

Cov.:

AF XY:

0.0326

AC XY:

5243

AN XY:

160980

show subpopulations

Gnomad4 AFR exome

AF:

0.0721

Gnomad4 AMR exome

AF:

0.0218

Gnomad4 ASJ exome

AF:

0.0199

Gnomad4 EAS exome

AF:

0.0269

Gnomad4 SAS exome

AF:

0.0142

Gnomad4 FIN exome

AF:

0.0559

Gnomad4 NFE exome

AF:

0.0381

Gnomad4 OTH exome

AF:

0.0427

GnomAD4 genome

AF:

0.0350

AC:

4459

AN:

127502

Hom.:

Cov.:

AF XY:

0.0349

AC XY:

2136

AN XY:

61196

show subpopulations

Gnomad4 AFR

AF:

0.0564

Gnomad4 AMR

AF:

0.0263

Gnomad4 ASJ

AF:

0.0136

Gnomad4 EAS

AF:

0.0216

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.0409

Gnomad4 NFE

AF:

0.0274

Gnomad4 OTH

AF:

0.0353

Alfa

AF:

0.0303

Hom.:

Bravo

AF:

0.0330

Asia WGS

AF:

0.0160

AC:

AN:

3218

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 19, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

5.4

DANN

Benign

0.66

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over