Variant chrX-48903516-C-T 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_001282651.2(SLC35A2):c.*1211G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 563,315 control chromosomes in the GnomAD database, including 32,580 homozygotes. There are 82,019 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.40 ( 6467 hom., 13117 hem., cov: 23)

Exomes 𝑓: 0.42 ( 26113 hom. 68902 hem. )

Consequence

SLC35A2
NM_001282651.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.433

Variant links:

Genes affected

SLC35A2 (HGNC:11022): (solute carrier family 35 member A2) This gene encodes a member of the nucleotide-sugar transporter family. The encoded protein is a multi-pass membrane protein. It transports UDP-galactose from the cytosol into Golgi vesicles, where it serves as a glycosyl donor for the generation of glycans. Mutations in this gene cause congenital disorder of glycosylation type IIm (CDG2M). Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Oct 2014]

SLC35A2 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=-0.84).

BP6

Variant X-48903516-C-T is Benign according to our data. Variant chrX-48903516-C-T is described in ClinVar as [Benign]. Clinvar id is 1245601.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A2	NM_005660.3 link	c.1164-51G>A		intron_variant	Intron 4 of 4	ENST00000247138.11	NP_005651.1	P78381-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A2	ENST00000247138.11 link	c.1164-51G>A		intron_variant	Intron 4 of 4	1	NM_005660.3	ENSP00000247138.5		P78381-1

Frequencies

GnomAD3 genomes

AF:

0.405

AC:

44632

AN:

110316

Hom.:

6466

Cov.:

AF XY:

0.402

AC XY:

13099

AN XY:

32598

show subpopulations

Gnomad AFR

AF:

0.375

Gnomad AMI

AF:

0.724

Gnomad AMR

AF:

0.388

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.599

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.406

Gnomad MID

AF:

0.401

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.401

GnomAD3 exomes

AF:

0.416

AC:

66787

AN:

160412

Hom.:

9743

AF XY:

0.418

AC XY:

20712

AN XY:

49538

show subpopulations

Gnomad AFR exome

AF:

0.377

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.374

Gnomad EAS exome

AF:

0.619

Gnomad SAS exome

AF:

0.390

Gnomad FIN exome

AF:

0.425

Gnomad NFE exome

AF:

0.418

Gnomad OTH exome

AF:

0.419

GnomAD4 exome

AF:

0.421

AC:

190711

AN:

452946

Hom.:

26113

Cov.:

AF XY:

0.424

AC XY:

68902

AN XY:

162638

show subpopulations

Gnomad4 AFR exome

AF:

0.371

Gnomad4 AMR exome

AF:

0.356

Gnomad4 ASJ exome

AF:

0.377

Gnomad4 EAS exome

AF:

0.622

Gnomad4 SAS exome

AF:

0.397

Gnomad4 FIN exome

AF:

0.425

Gnomad4 NFE exome

AF:

0.417

Gnomad4 OTH exome

AF:

0.421

GnomAD4 genome

AF:

0.404

AC:

44642

AN:

110369

Hom.:

6467

Cov.:

AF XY:

0.402

AC XY:

13117

AN XY:

32661

show subpopulations

Gnomad4 AFR

AF:

0.375

Gnomad4 AMR

AF:

0.389

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.599

Gnomad4 SAS

AF:

0.406

Gnomad4 FIN

AF:

0.406

Gnomad4 NFE

AF:

0.410

Gnomad4 OTH

AF:

0.397

Alfa

AF:

0.410

Hom.:

26383

Bravo

AF:

0.406

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

Jul 15, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 22% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 20. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.64

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