6-87477166-GGTGTGTGTGT-GGTGTGTGTGTGTGTGT

Variant names:

• chr6-87477166-G-GGTGTGT
• rs71018020
• NM_006416.5:c.17-176_17-171dupTGTGTG

Variant summary

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

The NM_006416.5(SLC35A1):​c.17-176_17-171dupTGTGTG 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 0.034 (144 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 = 0.0804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-176_17-171dupTGTGTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-176_17-171dupTGTGTG		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_17-195insGTGTGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-196_*61-195insGTGTGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.0341 AC: 5099 AN: 149724 Hom.: 143 Cov.: 0

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.00221

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.00547

Gnomad SAS AF: 0.0490

Gnomad FIN AF: 0.00299

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0341 AC: 5106 AN: 149828 Hom.: 144 Cov.: 0 AF XY: 0.0340 AC XY: 2480 AN XY: 73012

Gnomad4 AFR AF: 0.0827

Gnomad4 AMR AF: 0.0227

Gnomad4 ASJ AF: 0.0110

Gnomad4 EAS AF: 0.00549

Gnomad4 SAS AF: 0.0491

Gnomad4 FIN AF: 0.00299

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0247

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;