6-87477166-GGTGTGTGTGT-GGTGTGTGT

Variant names:

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

Variant summary

Our verdict is Uncertain significance. Variant got 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

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]

ENSG00000213204 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-172_17-171delTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-172_17-171delTG		intron_variant	Intron 1 of 6		NP_001161870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-195_17-194delGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-195_*61-194delGT		intron_variant	Intron 13 of 15	2		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

Gnomad4 AFR AF: 0.000612

Gnomad4 AMR AF: 0.000733

Gnomad4 ASJ AF: 0.000290

Gnomad4 EAS AF: 0.000784

Gnomad4 SAS AF: 0.000211

Gnomad4 FIN AF: 0.00492

Gnomad4 NFE AF: 0.00156

Gnomad4 OTH AF: 0.000484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs71018020; hg19: chr6-88186884;