6-87477166-G-GGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_006416.5(SLC35A1):c.17-178_17-171dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.041 (193 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-87477166-G-GGTGTGTGT is Benign according to our data. Variant chr6-87477166-G-GGTGTGTGT is described in ClinVar as [Benign]. Clinvar id is 1257149.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A1	NM_006416.5	c.17-178_17-171dup		intron_variant		ENST00000369552.9
SLC35A1	NM_001168398.2	c.17-178_17-171dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9	c.17-178_17-171dup		intron_variant		1	NM_006416.5	P1
SLC35A1	ENST00000369556.7	c.17-178_17-171dup		intron_variant		1
SLC35A1	ENST00000369557.9	c.17-178_17-171dup		intron_variant		2
SLC35A1	ENST00000464978.5	n.92-178_92-171dup		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6097 AN: 149730 Hom.: 188 Cov.: 0

Gnomad AFR AF: 0.0880

Gnomad AMI AF: 0.0397

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.00958

Gnomad EAS AF: 0.0115

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0298

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

GnomAD4 genome AF: 0.0409 AC: 6123 AN: 149834 Hom.: 193 Cov.: 0 AF XY: 0.0411 AC XY: 3001 AN XY: 73008

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.0264

Gnomad4 ASJ AF: 0.00958

Gnomad4 EAS AF: 0.0118

Gnomad4 SAS AF: 0.0194

Gnomad4 FIN AF: 0.0357

Gnomad4 NFE AF: 0.0219

Gnomad4 OTH AF: 0.0295

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 04, 2021

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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;