6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGT

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006416.5(SLC35A1):​c.17-180_17-171dupTGTGTGTGTG 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 0.022 (117 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-180_17-171dupTGTGTGTGTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-180_17-171dupTGTGTGTGTG		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.17-196_17-195insGTGTGTGTGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-196_*61-195insGTGTGTGTGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.0219 AC: 3279 AN: 149740 Hom.: 117 Cov.: 0

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00754

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00313

Gnomad SAS AF: 0.00126

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000297

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0219 AC: 3288 AN: 149844 Hom.: 117 Cov.: 0 AF XY: 0.0213 AC XY: 1554 AN XY: 73024

Gnomad4 AFR AF: 0.0756

Gnomad4 AMR AF: 0.00753

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00313

Gnomad4 SAS AF: 0.00126

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000297

Gnomad4 OTH AF: 0.0208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;