NM_006416.5:c.17-172_17-171delTG

Variant names:

• chr6-87477166-GGT-G
• rs71018020
• NM_006416.5:c.17-172_17-171delTG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_006416.5(SLC35A1):​c.17-172_17-171delTG 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 0.0013 (1 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: Uncertain_significance. The variant received 0 ACMG points.

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.17-172_17-171delTG		intron	N/A	NP_006407.1	P78382-1
	SLC35A1	NM_001168398.2		c.17-172_17-171delTG		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.17-195_17-194delGT		intron	N/A	ENSP00000358565.4	P78382-1
	SLC35A1	ENST00000369556.7	TSL:1	c.17-195_17-194delGT		intron	N/A	ENSP00000358569.3	P78382-2
	ENSG00000213204	ENST00000507897.5	TSL:2	n.*61-195_*61-194delGT		intron	N/A	ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00132 AC: 197 AN: 149614 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.000614

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000734

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.000782

Gnomad SAS AF: 0.000210

Gnomad FIN AF: 0.00492

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00156

Gnomad OTH AF: 0.000487

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

GnomAD4 genome AF: 0.00132 AC: 197 AN: 149716 Hom.: 1 Cov.: 0 AF XY: 0.00160 AC XY: 117 AN XY: 72950

African (AFR) AF: 0.000612 AC: 25 AN: 40844

American (AMR) AF: 0.000733 AC: 11 AN: 15006

Ashkenazi Jewish (ASJ) AF: 0.000290 AC: 1 AN: 3444

East Asian (EAS) AF: 0.000784 AC: 4 AN: 5100

South Asian (SAS) AF: 0.000211 AC: 1 AN: 4748

European-Finnish (FIN) AF: 0.00492 AC: 49 AN: 9960

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00156 AC: 105 AN: 67346

Other (OTH) AF: 0.000484 AC: 1 AN: 2068

Alfa AF: 0.00226 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

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

Other links and lift over

dbSNP: rs71018020; hg19: chr6-88186884; COSMIC: COSV65780335; COSMIC: COSV65780335;