6-87472986-G-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.-18G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 657,550 control chromosomes in the GnomAD database, including 101,285 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.62 ( 30014 hom., cov: 34)

Exomes 𝑓: 0.52 ( 71271 hom. )

Consequence

SLC35A1
NM_006416.5 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.620

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:

LOC124901357 (HGNC:):

LOC124901357 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=-0.77).

BP6

Variant 6-87472986-G-C is Benign according to our data. Variant chr6-87472986-G-C is described in ClinVar as [Benign]. Clinvar id is 95391.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
SLC35A1	NM_006416.5 linkuse as main transcript	c.-18G>C	5_prime_UTR_variant	1/8	ENST00000369552.9
SLC35A1	NM_001168398.2 linkuse as main transcript	c.-18G>C	5_prime_UTR_variant	1/7
LOC124901357	XR_007059668.1 linkuse as main transcript		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9 linkuse as main transcript	c.-18G>C	5_prime_UTR_variant	1/8	1	NM_006416.5	P1	P78382-1
SLC35A1	ENST00000369556.7 linkuse as main transcript	c.-18G>C	5_prime_UTR_variant	1/7	1			P78382-2
SLC35A1	ENST00000369557.9 linkuse as main transcript	c.-18G>C	5_prime_UTR_variant	1/6	2
SLC35A1	ENST00000464978.5 linkuse as main transcript	n.91+2273G>C	intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93553

AN:

152000

Hom.:

29958

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.598

Gnomad AMR

AF:

0.681

Gnomad ASJ

AF:

0.491

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.564

Gnomad FIN

AF:

0.481

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.532

Gnomad OTH

AF:

0.603

GnomAD3 exomes

AF:

0.598

AC:

7759

AN:

12976

Hom.:

2345

AF XY:

0.582

AC XY:

3758

AN XY:

6454

show subpopulations

Gnomad AFR exome

AF:

0.826

Gnomad AMR exome

AF:

0.699

Gnomad ASJ exome

AF:

0.514

Gnomad EAS exome

AF:

0.520

Gnomad SAS exome

AF:

0.581

Gnomad FIN exome

AF:

0.606

Gnomad NFE exome

AF:

0.561

Gnomad OTH exome

AF:

0.554

GnomAD4 exome

AF:

0.525

AC:

265277

AN:

505432

Hom.:

71271

Cov.:

AF XY:

0.525

AC XY:

137165

AN XY:

261452

show subpopulations

Gnomad4 AFR exome

AF:

0.786

Gnomad4 AMR exome

AF:

0.693

Gnomad4 ASJ exome

AF:

0.480

Gnomad4 EAS exome

AF:

0.513

Gnomad4 SAS exome

AF:

0.540

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.513

Gnomad4 OTH exome

AF:

0.552

GnomAD4 genome

AF:

0.616

AC:

93671

AN:

152118

Hom.:

30014

Cov.:

AF XY:

0.613

AC XY:

45548

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.793

Gnomad4 AMR

AF:

0.682

Gnomad4 ASJ

AF:

0.491

Gnomad4 EAS

AF:

0.510

Gnomad4 SAS

AF:

0.563

Gnomad4 FIN

AF:

0.481

Gnomad4 NFE

AF:

0.532

Gnomad4 OTH

AF:

0.606

Alfa

AF:

0.439

Hom.:

1175

Bravo

AF:

0.641

Asia WGS

AF:

0.615

AC:

2135

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

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. -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jan 20, 2016	- -

SLC35A1-congenital disorder of glycosylation

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

Cadd

Benign

Dann

Benign

0.79

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.14

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