rs146079657
Positions:
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005660.3(SLC35A2):c.990C>T(p.Leu330=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000867 in 1,208,994 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 361 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00065 ( 0 hom., 27 hem., cov: 23)
Exomes 𝑓: 0.00089 ( 0 hom. 334 hem. )
Consequence
SLC35A2
NM_005660.3 synonymous
NM_005660.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.292
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
?
Variant X-48904919-G-A is Benign according to our data. Variant chrX-48904919-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 383041.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.292 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 27 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A2 | NM_005660.3 | c.990C>T | p.Leu330= | synonymous_variant | 4/5 | ENST00000247138.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A2 | ENST00000247138.11 | c.990C>T | p.Leu330= | synonymous_variant | 4/5 | 1 | NM_005660.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000651 AC: 73AN: 112132Hom.: 0 Cov.: 23 AF XY: 0.000788 AC XY: 27AN XY: 34278
GnomAD3 genomes
?
AF:
AC:
73
AN:
112132
Hom.:
Cov.:
23
AF XY:
AC XY:
27
AN XY:
34278
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000567 AC: 102AN: 180043Hom.: 0 AF XY: 0.000695 AC XY: 45AN XY: 64769
GnomAD3 exomes
AF:
AC:
102
AN:
180043
Hom.:
AF XY:
AC XY:
45
AN XY:
64769
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000889 AC: 975AN: 1096862Hom.: 0 Cov.: 31 AF XY: 0.000922 AC XY: 334AN XY: 362242
GnomAD4 exome
AF:
AC:
975
AN:
1096862
Hom.:
Cov.:
31
AF XY:
AC XY:
334
AN XY:
362242
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.000651 AC: 73AN: 112132Hom.: 0 Cov.: 23 AF XY: 0.000788 AC XY: 27AN XY: 34278
GnomAD4 genome
?
AF:
AC:
73
AN:
112132
Hom.:
Cov.:
23
AF XY:
AC XY:
27
AN XY:
34278
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
SLC35A2-congenital disorder of glycosylation Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 09, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 17, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2017 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
BranchPoint Hunter
?
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at