rs375311728
Positions:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_005660.3(SLC35A2):āc.750C>Gā(p.Leu250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000488 in 1,208,949 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.00012 ( 0 hom., 4 hem., cov: 24)
Exomes š: 0.000041 ( 0 hom. 17 hem. )
Consequence
SLC35A2
NM_005660.3 synonymous
NM_005660.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.764
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BP6
?
Variant X-48905159-G-C is Benign according to our data. Variant chrX-48905159-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 541107.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.764 with no splicing effect.
BS2
?
High Hemizygotes in GnomAd4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A2 | NM_005660.3 | c.750C>G | p.Leu250= | synonymous_variant | 4/5 | ENST00000247138.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A2 | ENST00000247138.11 | c.750C>G | p.Leu250= | synonymous_variant | 4/5 | 1 | NM_005660.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000124 AC: 14AN: 112678Hom.: 0 Cov.: 24 AF XY: 0.000115 AC XY: 4AN XY: 34812
GnomAD3 genomes
?
AF:
AC:
14
AN:
112678
Hom.:
Cov.:
24
AF XY:
AC XY:
4
AN XY:
34812
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: 0.0000798 AC: 14AN: 175483Hom.: 0 AF XY: 0.0000649 AC XY: 4AN XY: 61655
GnomAD3 exomes
AF:
AC:
14
AN:
175483
Hom.:
AF XY:
AC XY:
4
AN XY:
61655
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: 0.0000411 AC: 45AN: 1096216Hom.: 0 Cov.: 31 AF XY: 0.0000470 AC XY: 17AN XY: 361850
GnomAD4 exome
AF:
AC:
45
AN:
1096216
Hom.:
Cov.:
31
AF XY:
AC XY:
17
AN XY:
361850
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: 0.000124 AC: 14AN: 112733Hom.: 0 Cov.: 24 AF XY: 0.000115 AC XY: 4AN XY: 34877
GnomAD4 genome
?
AF:
AC:
14
AN:
112733
Hom.:
Cov.:
24
AF XY:
AC XY:
4
AN XY:
34877
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SLC35A2-congenital disorder of glycosylation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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