chr6-87511385-T-C

Position:

chr6-87511385-T-C

Variant summary

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

The NM_006416.5(SLC35A1):c.887-14T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 1,612,446 control chromosomes in the GnomAD database, including 8,338 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 924 hom., cov: 32)

Exomes 𝑓: 0.099 ( 7414 hom. )

Consequence

SLC35A1
NM_006416.5 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.116

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-87511385-T-C is Benign according to our data. Variant chr6-87511385-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 95394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 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.887-14T>C		splice_polypyrimidine_tract_variant, intron_variant		ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2 linkuse as main transcript	c.710-14T>C		splice_polypyrimidine_tract_variant, intron_variant			NP_001161870.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SLC35A1	ENST00000369552.9 linkuse as main transcript	c.887-14T>C	splice_polypyrimidine_tract_variant, intron_variant	1	NM_006416.5	ENSP00000358565	P1	P78382-1
SLC35A1	ENST00000369556.7 linkuse as main transcript	c.710-14T>C	splice_polypyrimidine_tract_variant, intron_variant	1		ENSP00000358569		P78382-2
SLC35A1	ENST00000369557.9 linkuse as main transcript	c.*73-14T>C	splice_polypyrimidine_tract_variant, intron_variant	2		ENSP00000358570
SLC35A1	ENST00000464978.5 linkuse as main transcript	n.895-14T>C	splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16347

AN:

152030

Hom.:

923

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.125

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0867

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.0968

Gnomad OTH

AF:

0.106

GnomAD3 exomes

AF:

0.106

AC:

26629

AN:

251038

Hom.:

1489

AF XY:

0.105

AC XY:

14225

AN XY:

135740

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.0869

Gnomad EAS exome

AF:

0.168

Gnomad SAS exome

AF:

0.0981

Gnomad FIN exome

AF:

0.0980

Gnomad NFE exome

AF:

0.0975

Gnomad OTH exome

AF:

0.104

GnomAD4 exome

AF:

0.0987

AC:

144101

AN:

1460298

Hom.:

7414

Cov.:

AF XY:

0.0984

AC XY:

71462

AN XY:

726540

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.117

Gnomad4 ASJ exome

AF:

0.0869

Gnomad4 EAS exome

AF:

0.154

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.0994

Gnomad4 NFE exome

AF:

0.0952

Gnomad4 OTH exome

AF:

0.101

GnomAD4 genome

AF:

0.108

AC:

16366

AN:

152148

Hom.:

924

Cov.:

AF XY:

0.107

AC XY:

7989

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.116

Gnomad4 AMR

AF:

0.126

Gnomad4 ASJ

AF:

0.0867

Gnomad4 EAS

AF:

0.155

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0969

Gnomad4 OTH

AF:

0.108

Alfa

AF:

0.0966

Hom.:

189

Bravo

AF:

0.113

Asia WGS

AF:

0.143

AC:

499

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Mar 29, 2016	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 09, 2012	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 02, 2015	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. -

SLC35A1-congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 29, 2024

- -

Congenital disorder of glycosylation

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

not provided

Benign:1

Likely benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Pontoneocerebellar hypoplasia

Benign:1

Likely 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

-0.81

CADD

Benign

1.1

DANN

Benign

0.71

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