6-87472981-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_006416.5(SLC35A1):c.-23C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000105 in 659,522 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000085 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
SLC35A1
NM_006416.5 5_prime_UTR
NM_006416.5 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 1.36
Genes affected
SLC35A1 (HGNC:11021): (solute carrier family 35 member A1) The protein encoded by this gene is found in the membrane of the Golgi apparatus, where it transports nucleotide sugars into the Golgi. One such nucleotide sugar is CMP-sialic acid, which is imported into the Golgi by the encoded protein and subsequently glycosylated. Defects in this gene are a cause of congenital disorder of glycosylation type 2F (CDG2F). Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Dec 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
Variant 6-87472981-C-T is Benign according to our data. Variant chr6-87472981-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 383666.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC35A1 | NM_006416.5 | c.-23C>T | 5_prime_UTR_variant | 1/8 | ENST00000369552.9 | ||
SLC35A1 | NM_001168398.2 | c.-23C>T | 5_prime_UTR_variant | 1/7 | |||
LOC124901357 | XR_007059668.1 | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC35A1 | ENST00000369552.9 | c.-23C>T | 5_prime_UTR_variant | 1/8 | 1 | NM_006416.5 | P1 | ||
SLC35A1 | ENST00000369556.7 | c.-23C>T | 5_prime_UTR_variant | 1/7 | 1 | ||||
SLC35A1 | ENST00000369557.9 | c.-23C>T | 5_prime_UTR_variant | 1/6 | 2 | ||||
SLC35A1 | ENST00000464978.5 | n.91+2268C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152196Hom.: 0 Cov.: 34
GnomAD3 genomes
?
AF:
AC:
13
AN:
152196
Hom.:
Cov.:
34
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:
GnomAD4 exome AF: 0.000110 AC: 56AN: 507208Hom.: 0 Cov.: 6 AF XY: 0.000141 AC XY: 37AN XY: 263222
GnomAD4 exome
AF:
AC:
56
AN:
507208
Hom.:
Cov.:
6
AF XY:
AC XY:
37
AN XY:
263222
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: 0.0000854 AC: 13AN: 152314Hom.: 0 Cov.: 34 AF XY: 0.0000940 AC XY: 7AN XY: 74462
GnomAD4 genome
?
AF:
AC:
13
AN:
152314
Hom.:
Cov.:
34
AF XY:
AC XY:
7
AN XY:
74462
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
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 19, 2018 | 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. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
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