chrX-48904641-C-T
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The ENST00000445167.7(SLC35A2):c.678G>A(p.Pro226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000299 in 1,206,007 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 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 0.000027 ( 0 hom., 1 hem., cov: 23)
Exomes 𝑓: 0.000030 ( 0 hom. 11 hem. )
Consequence
SLC35A2
ENST00000445167.7 synonymous
ENST00000445167.7 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.260
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant X-48904641-C-T is Benign according to our data. Variant chrX-48904641-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660485.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.26 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 11 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A2 | NM_005660.3 | c.1163+105G>A | intron_variant | ENST00000247138.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A2 | ENST00000247138.11 | c.1163+105G>A | intron_variant | 1 | NM_005660.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112244Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34380
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GnomAD3 exomes AF: 0.0000118 AC: 2AN: 169801Hom.: 0 AF XY: 0.0000177 AC XY: 1AN XY: 56545
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GnomAD4 exome AF: 0.0000302 AC: 33AN: 1093763Hom.: 0 Cov.: 31 AF XY: 0.0000306 AC XY: 11AN XY: 359609
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GnomAD4 genome AF: 0.0000267 AC: 3AN: 112244Hom.: 0 Cov.: 23 AF XY: 0.0000291 AC XY: 1AN XY: 34380
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | SLC35A2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at