6-87477166-G-GGT

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_006416.5(SLC35A1):​c.17-172_17-171dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0071 (3 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 6-87477166-G-GGT is Benign according to our data. Variant chr6-87477166-G-GGT is described in ClinVar as Likely_benign. ClinVar VariationId is 1198731.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 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.17-172_17-171dupTG		intron	N/A	NP_006407.1	P78382-1
	SLC35A1	NM_001168398.2		c.17-172_17-171dupTG		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_17-195insGT		intron	N/A	ENSP00000358565.4	P78382-1
	SLC35A1	ENST00000369556.7	TSL:1	c.17-196_17-195insGT		intron	N/A	ENSP00000358569.3	P78382-2
	ENSG00000213204	ENST00000507897.5	TSL:2	n.*61-196_*61-195insGT		intron	N/A	ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00709 AC: 1061 AN: 149584 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0254

Gnomad AMR AF: 0.00515

Gnomad ASJ AF: 0.0102

Gnomad EAS AF: 0.00469

Gnomad SAS AF: 0.00694

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.00634

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

GnomAD4 genome AF: 0.00714 AC: 1068 AN: 149684 Hom.: 3 Cov.: 0 AF XY: 0.00695 AC XY: 507 AN XY: 72926

African (AFR) AF: 0.0106 AC: 433 AN: 40848

American (AMR) AF: 0.00521 AC: 78 AN: 14982

Ashkenazi Jewish (ASJ) AF: 0.0102 AC: 35 AN: 3446

East Asian (EAS) AF: 0.00490 AC: 25 AN: 5098

South Asian (SAS) AF: 0.00716 AC: 34 AN: 4746

European-Finnish (FIN) AF: 0.00211 AC: 21 AN: 9968

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

European-Non Finnish (NFE) AF: 0.00603 AC: 406 AN: 67332

Other (OTH) AF: 0.00630 AC: 13 AN: 2064

Alfa AF: 0.00493 Hom.: 299

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

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;