chr7-134295047-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_032826.5(SLC35B4):c.782C>G(p.Thr261Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,614,196 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00029 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000031 ( 0 hom. )
Consequence
SLC35B4
NM_032826.5 missense
NM_032826.5 missense
Scores
3
8
8
Clinical Significance
Conservation
PhyloP100: 10.0
Genes affected
SLC35B4 (HGNC:20584): (solute carrier family 35 member B4) Glycosyltransferases, such as SLC35B4, transport nucleotide sugars from the cytoplasm where they are synthesized, to the Golgi apparatus where they are utilized in the synthesis of glycoproteins, glycolipids, and proteoglycans (Ashikov et al., 2005 [PubMed 15911612]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35B4 | NM_032826.5 | c.782C>G | p.Thr261Ser | missense_variant | 10/10 | ENST00000378509.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35B4 | ENST00000378509.9 | c.782C>G | p.Thr261Ser | missense_variant | 10/10 | 1 | NM_032826.5 | P1 | |
SLC35B4 | ENST00000416907.5 | c.*333C>G | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 1 | ||||
SLC35B4 | ENST00000466599.1 | n.98+33C>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152202Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251298Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135832
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GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727236
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GnomAD4 genome ? AF: 0.000289 AC: 44AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74502
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ExAC
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2022 | The c.782C>G (p.T261S) alteration is located in exon 10 (coding exon 10) of the SLC35B4 gene. This alteration results from a C to G substitution at nucleotide position 782, causing the threonine (T) at amino acid position 261 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Uncertain
Dann
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Loss of glycosylation at T261 (P = 0.0969);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at