6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGT

Variant names:

• chr6-87477166-G-GGTGTGT
• rs71018020
• NM_006416.5:c.17-176_17-171dupTGTGTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006416.5(SLC35A1):​c.17-176_17-171dupTGTGTG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.034 (144 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 0 publications found

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

ENSG00000213204 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0804 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.17-176_17-171dupTGTGTG		intron	N/A	NP_006407.1	P78382-1
	SLC35A1	NM_001168398.2		c.17-176_17-171dupTGTGTG		intron	N/A	NP_001161870.1	P78382-2

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5099 AN: 149724 Hom.: 143 Cov.: 0

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.00221

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00547

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.00299

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0341 AC: 5106 AN: 149828 Hom.: 144 Cov.: 0 AF XY: 0.0340 AC XY: 2480 AN XY: 73012

African (AFR) AF: 0.0827 AC: 3378 AN: 40832

American (AMR) AF: 0.0227 AC: 340 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3446

East Asian (EAS) AF: 0.00549 AC: 28 AN: 5102

South Asian (SAS) AF: 0.0491 AC: 233 AN: 4746

European-Finnish (FIN) AF: 0.00299 AC: 30 AN: 10022

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0148 AC: 1000 AN: 67402

Other (OTH) AF: 0.0247 AC: 51 AN: 2068

Alfa AF: 0.00426 Hom.: 299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.078
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs71018020; hg19: chr6-88186884;