Genetic Variant SLC35A1:c.17-174_17-171dupTGTG (chr6-87477166-G-GGTGT) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006416.5(SLC35A1):c.17-174_17-171dupTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.37 ( 10103 hom., cov: 0)

Consequence

SLC35A1
NM_006416.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0780

Publications

0 publications found

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 Gene-Disease associations (from GenCC):

SLC35A1-congenital disorder of glycosylation
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), PanelApp Australia, G2P

SLC35A1 links:

ENSG00000213204 (HGNC:):

ENSG00000213204 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant 6-87477166-G-GGTGT is Benign according to our data. Variant chr6-87477166-G-GGTGT is described in ClinVar as Benign. ClinVar VariationId is 1174350.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006416.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35A1	NM_006416.5	MANE Select	c.17-174_17-171dupTGTG		intron	N/A	NP_006407.1	P78382-1
	SLC35A1	NM_001168398.2		c.17-174_17-171dupTGTG		intron	N/A	NP_001161870.1	P78382-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC35A1	ENST00000369552.9	TSL:1 MANE Select	c.17-196_17-195insGTGT	intron	N/A	ENSP00000358565.4	P78382-1
SLC35A1	ENST00000369556.7	TSL:1	c.17-196_17-195insGTGT	intron	N/A	ENSP00000358569.3	P78382-2
ENSG00000213204	ENST00000507897.5	TSL:2	n.61-196_61-195insGTGT	intron	N/A	ENSP00000426769.1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

55210

AN:

149604

Hom.:

10096

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.362

Gnomad AMR

AF:

0.476

Gnomad ASJ

AF:

0.361

Gnomad EAS

AF:

0.382

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.375

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.380

Gnomad OTH

AF:

0.388

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.369

AC:

55228

AN:

149708

Hom.:

10103

Cov.:

AF XY:

0.370

AC XY:

26961

AN XY:

72938

show subpopulations

African (AFR)

AF:

0.305

AC:

12461

AN:

40790

American (AMR)

AF:

0.477

AC:

7145

AN:

14984

Ashkenazi Jewish (ASJ)

AF:

0.361

AC:

1245

AN:

3446

East Asian (EAS)

AF:

0.383

AC:

1952

AN:

5100

South Asian (SAS)

AF:

0.383

AC:

1819

AN:

4744

European-Finnish (FIN)

AF:

0.375

AC:

3748

AN:

10000

Middle Eastern (MID)

AF:

0.408

AC:

120

AN:

294

European-Non Finnish (NFE)

AF:

0.380

AC:

25606

AN:

67380

Other (OTH)

AF:

0.390

AC:

805

AN:

2066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1697

3394

5090

6787

8484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

538

1076

1614

2152

2690

<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:

0.228

Hom.:

299

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.078

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over