6-87477166-GGTGTGTGTGT-GGTGTGT

Variant names:

• chr6-87477166-GGTGT-G
• rs71018020
• NM_006416.5:c.17-174_17-171delTGTG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006416.5(SLC35A1):​c.17-174_17-171delTGTG 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 0.0050 (5 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-174_17-171delTGTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-174_17-171delTGTG		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_17-192delGTGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-195_*61-192delGTGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00499 AC: 747 AN: 149762 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.0146

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00427

Gnomad ASJ AF: 0.000871

Gnomad EAS AF: 0.000977

Gnomad SAS AF: 0.00147

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.000727

Gnomad OTH AF: 0.00877

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

GnomAD4 genome AF: 0.00503 AC: 754 AN: 149866 Hom.: 5 Cov.: 0 AF XY: 0.00493 AC XY: 360 AN XY: 73032

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.00426

Gnomad4 ASJ AF: 0.000871

Gnomad4 EAS AF: 0.000980

Gnomad4 SAS AF: 0.00147

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000727

Gnomad4 OTH AF: 0.00870

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;