Genetic Variant SLC35C1:c.-32+493A>G (chr11-45805010-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001425155.1(SLC35C1):c.-220+493A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.068 in 985,680 control chromosomes in the GnomAD database, including 2,519 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 310 hom., cov: 33)

Exomes 𝑓: 0.071 ( 2209 hom. )

Consequence

SLC35C1
NM_001425155.1 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.13

Publications

0 publications found

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:

LINC02690 (HGNC:54194): (long intergenic non-protein coding RNA 2690)

LINC02690 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 11-45805010-A-G is Benign according to our data. Variant chr11-45805010-A-G is described in ClinVar as Benign. ClinVar VariationId is 1292087.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001425155.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC35C1	NM_001425155.1	c.-220+493A>G	intron	N/A	NP_001412084.1	B3KQH0
SLC35C1	NM_001145265.2	c.-32+493A>G	intron	N/A	NP_001138737.1	Q96A29-2
SLC35C1	NM_001145266.2	c.-32+590A>G	intron	N/A	NP_001138738.1	Q96A29-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC35C1	ENST00000442528.2	TSL:1	c.-32+493A>G	intron	N/A	ENSP00000412408.2	Q96A29-2
SLC35C1	ENST00000953729.1		c.-220+493A>G	intron	N/A	ENSP00000623788.1
SLC35C1	ENST00000526817.2	TSL:2	c.-32+590A>G	intron	N/A	ENSP00000432145.2	Q96A29-2

Frequencies

GnomAD3 genomes

AF:

0.0525

AC:

7989

AN:

152102

Hom.:

310

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0127

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.0452

Gnomad ASJ

AF:

0.0827

Gnomad EAS

AF:

0.000772

Gnomad SAS

AF:

0.00683

Gnomad FIN

AF:

0.108

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0754

Gnomad OTH

AF:

0.0516

GnomAD4 exome

AF:

0.0708

AC:

59008

AN:

833460

Hom.:

2209

Cov.:

AF XY:

0.0707

AC XY:

27238

AN XY:

384998

show subpopulations

African (AFR)

AF:

0.00829

AC:

131

AN:

15794

American (AMR)

AF:

0.0385

AC:

AN:

986

Ashkenazi Jewish (ASJ)

AF:

0.0766

AC:

395

AN:

5154

East Asian (EAS)

AF:

0.00165

AC:

AN:

3642

South Asian (SAS)

AF:

0.00758

AC:

125

AN:

16496

European-Finnish (FIN)

AF:

0.121

AC:

AN:

282

Middle Eastern (MID)

AF:

0.0111

AC:

AN:

1626

European-Non Finnish (NFE)

AF:

0.0745

AC:

56786

AN:

762170

Other (OTH)

AF:

0.0540

AC:

1475

AN:

27310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

3568

7135

10703

14270

17838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2828

5656

8484

11312

14140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0525

AC:

7986

AN:

152220

Hom.:

310

Cov.:

AF XY:

0.0518

AC XY:

3859

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0127

AC:

526

AN:

41542

American (AMR)

AF:

0.0450

AC:

689

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0827

AC:

287

AN:

3472

East Asian (EAS)

AF:

0.000774

AC:

AN:

5166

South Asian (SAS)

AF:

0.00705

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.108

AC:

1149

AN:

10612

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0754

AC:

5123

AN:

67980

Other (OTH)

AF:

0.0511

AC:

108

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

410

819

1229

1638

2048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0641

Hom.:

Bravo

AF:

0.0464

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.25

(source)

DANN

Benign

0.38

PhyloP100

-1.1

PromoterAI

-0.035

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over