Variant rs1051131 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000369552.9(SLC35A1):c.*302A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 381,954 control chromosomes in the GnomAD database, including 64,973 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 29023 hom., cov: 31)

Exomes 𝑓: 0.55 ( 35950 hom. )

Consequence

SLC35A1
ENST00000369552.9 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.629

Variant links:

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]

SLC35A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 6-87511828-A-G is Benign according to our data. Variant chr6-87511828-A-G is described in ClinVar as [Benign]. Clinvar id is 358221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.746 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC35A1	NM_006416.5 linkuse as main transcript	c.*302A>G		3_prime_UTR_variant	8/8	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2 linkuse as main transcript	c.*302A>G		3_prime_UTR_variant	7/7		NP_001161870.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC35A1	ENST00000369552.9 linkuse as main transcript	c.*302A>G	3_prime_UTR_variant	8/8	1	NM_006416.5	ENSP00000358565	P1	P78382-1
SLC35A1	ENST00000369556.7 linkuse as main transcript	c.*302A>G	3_prime_UTR_variant	7/7	1		ENSP00000358569		P78382-2
SLC35A1	ENST00000369557.9 linkuse as main transcript	c.*502A>G	3_prime_UTR_variant	6/6	2		ENSP00000358570
SLC35A1	ENST00000464978.5 linkuse as main transcript		downstream_gene_variant		2

Frequencies

GnomAD3 genomes

AF:

0.609

AC:

92508

AN:

151868

Hom.:

28975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.753

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.492

Gnomad EAS

AF:

0.562

Gnomad SAS

AF:

0.568

Gnomad FIN

AF:

0.520

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.597

GnomAD4 exome

AF:

0.555

AC:

127542

AN:

229966

Hom.:

35950

Cov.:

AF XY:

0.553

AC XY:

69266

AN XY:

125240

show subpopulations

Gnomad4 AFR exome

AF:

0.754

Gnomad4 AMR exome

AF:

0.683

Gnomad4 ASJ exome

AF:

0.495

Gnomad4 EAS exome

AF:

0.568

Gnomad4 SAS exome

AF:

0.560

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.534

Gnomad4 OTH exome

AF:

0.565

GnomAD4 genome

AF:

0.609

AC:

92621

AN:

151988

Hom.:

29023

Cov.:

AF XY:

0.608

AC XY:

45158

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.753

Gnomad4 AMR

AF:

0.677

Gnomad4 ASJ

AF:

0.492

Gnomad4 EAS

AF:

0.563

Gnomad4 SAS

AF:

0.567

Gnomad4 FIN

AF:

0.520

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.600

Alfa

AF:

0.573

Hom.:

9753

Bravo

AF:

0.629

Asia WGS

AF:

0.635

AC:

2204

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 27, 2018

- -

Pontoneocerebellar hypoplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.77

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over