rs71018020

Variant names:

• chr6-87477166-GGTGTGTGTGT-G
• rs71018020
• NM_006416.5:c.17-180_17-171delTGTGTGTGTG

Your query was ambiguous. Multiple possible variants found:

• chr6-87477166-GGTGTGTGTGT-G
• chr6-87477166-GGTGTGTGTGT-GGT
• chr6-87477166-GGTGTGTGTGT-GGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGT
• chr6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_006416.5(SLC35A1):​c.17-180_17-171delTGTGTGTGTG 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 0.0090 (8 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 8 AR gene

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.17-180_17-171delTGTGTGTGTG		intron	N/A	NP_006407.1	P78382-1
	SLC35A1	NM_001168398.2		c.17-180_17-171delTGTGTGTGTG		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_17-186delGTGTGTGTGT		intron	N/A	ENSP00000358565.4	P78382-1
	SLC35A1	ENST00000369556.7	TSL:1	c.17-195_17-186delGTGTGTGTGT		intron	N/A	ENSP00000358569.3	P78382-2
	ENSG00000213204	ENST00000507897.5	TSL:2	n.*61-195_*61-186delGTGTGTGTGT		intron	N/A	ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00899 AC: 1346 AN: 149768 Hom.: 8 Cov.: 0

Gnomad AFR AF: 0.00263

Gnomad AMI AF: 0.0574

Gnomad AMR AF: 0.00560

Gnomad ASJ AF: 0.0151

Gnomad EAS AF: 0.000391

Gnomad SAS AF: 0.00588

Gnomad FIN AF: 0.00419

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.00585

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

GnomAD4 genome AF: 0.00898 AC: 1346 AN: 149872 Hom.: 8 Cov.: 0 AF XY: 0.00849 AC XY: 620 AN XY: 73036

African (AFR) AF: 0.00262 AC: 107 AN: 40854

American (AMR) AF: 0.00560 AC: 84 AN: 15010

Ashkenazi Jewish (ASJ) AF: 0.0151 AC: 52 AN: 3446

East Asian (EAS) AF: 0.000392 AC: 2 AN: 5104

South Asian (SAS) AF: 0.00589 AC: 28 AN: 4750

European-Finnish (FIN) AF: 0.00419 AC: 42 AN: 10028

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0143 AC: 966 AN: 67412

Other (OTH) AF: 0.00580 AC: 12 AN: 2068

Alfa AF: 0.00453 Hom.: 299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.91
Mutation Taster		=96/4	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;