Genetic Variant NM_018389.5:c.536-32A>G (chr11-45810744-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_018389.5(SLC35C1):c.536-32A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 1,598,348 control chromosomes in the GnomAD database, including 25,520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.21 ( 3824 hom., cov: 33)

Exomes 𝑓: 0.17 ( 21696 hom. )

Consequence

SLC35C1
NM_018389.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -4.56

Variant links:

Genes affected

SLC35C1 (HGNC:20197): (solute carrier family 35 member C1) This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

SLC35C1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 3 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 11-45810744-A-G is Benign according to our data. Variant chr11-45810744-A-G is described in ClinVar as [Benign]. Clinvar id is 261027.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35C1	NM_018389.5 link	c.536-32A>G		intron_variant	Intron 1 of 1	ENST00000314134.4	NP_060859.4	Q96A29-1B3KQH0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SLC35C1	ENST00000314134.4 link	c.536-32A>G	intron_variant	Intron 1 of 1	1	NM_018389.5	ENSP00000313318.3	Q96A29-1
SLC35C1	ENST00000442528.2 link	c.497-32A>G	intron_variant	Intron 2 of 2	1		ENSP00000412408.2	Q96A29-2
SLC35C1	ENST00000526817.2 link	c.497-32A>G	intron_variant	Intron 2 of 2	2		ENSP00000432145.2	Q96A29-2E9PS26

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31747

AN:

151644

Hom.:

3819

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.0599

Gnomad SAS

AF:

0.0530

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.170

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.167

AC:

40554

AN:

242258

Hom.:

4012

AF XY:

0.156

AC XY:

20551

AN XY:

131396

show subpopulations

Gnomad AFR exome

AF:

0.322

Gnomad AMR exome

AF:

0.228

Gnomad ASJ exome

AF:

0.121

Gnomad EAS exome

AF:

0.0601

Gnomad SAS exome

AF:

0.0507

Gnomad FIN exome

AF:

0.228

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.161

GnomAD4 exome

AF:

0.166

AC:

240389

AN:

1446586

Hom.:

21696

Cov.:

AF XY:

0.161

AC XY:

115568

AN XY:

717636

show subpopulations

Gnomad4 AFR exome

AF:

0.327

Gnomad4 AMR exome

AF:

0.228

Gnomad4 ASJ exome

AF:

0.122

Gnomad4 EAS exome

AF:

0.0556

Gnomad4 SAS exome

AF:

0.0516

Gnomad4 FIN exome

AF:

0.230

Gnomad4 NFE exome

AF:

0.171

Gnomad4 OTH exome

AF:

0.163

GnomAD4 genome

AF:

0.209

AC:

31784

AN:

151762

Hom.:

3824

Cov.:

AF XY:

0.207

AC XY:

15389

AN XY:

74170

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.216

Gnomad4 ASJ

AF:

0.134

Gnomad4 EAS

AF:

0.0601

Gnomad4 SAS

AF:

0.0530

Gnomad4 FIN

AF:

0.223

Gnomad4 NFE

AF:

0.170

Gnomad4 OTH

AF:

0.184

Alfa

AF:

0.177

Hom.:

694

Bravo

AF:

0.215

Asia WGS

AF:

0.0890

AC:

312

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 29, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.023

DANN

Benign

0.23

La Branchor

0.67

BranchPoint Hunter

3.0

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