6-87477166-G-GGT

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_006416.5(SLC35A1):​c.17-172_17-171dupTG variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.0071 (3 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Likely 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]

ENSG00000213204 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 6-87477166-G-GGT is Benign according to our data. Variant chr6-87477166-G-GGT is described in ClinVar as [Likely_benign]. Clinvar id is 1198731.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC35A1	NM_006416.5	c.17-172_17-171dupTG		intron_variant	Intron 1 of 7	ENST00000369552.9	NP_006407.1
SLC35A1	NM_001168398.2	c.17-172_17-171dupTG		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_17-195insGT		intron_variant	Intron 1 of 7	1	NM_006416.5	ENSP00000358565.4
ENSG00000213204	ENST00000507897.5	n.*61-196_*61-195insGT		intron_variant	Intron 13 of 15	2		ENSP00000426769.1

Frequencies

GnomAD3 genomes AF: 0.00709 AC: 1061 AN: 149584 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0105

Gnomad AMI AF: 0.0254

Gnomad AMR AF: 0.00515

Gnomad ASJ AF: 0.0102

Gnomad EAS AF: 0.00469

Gnomad SAS AF: 0.00694

Gnomad FIN AF: 0.00211

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.00634

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

GnomAD4 genome AF: 0.00714 AC: 1068 AN: 149684 Hom.: 3 Cov.: 0 AF XY: 0.00695 AC XY: 507 AN XY: 72926

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.00521

Gnomad4 ASJ AF: 0.0102

Gnomad4 EAS AF: 0.00490

Gnomad4 SAS AF: 0.00716

Gnomad4 FIN AF: 0.00211

Gnomad4 NFE AF: 0.00603

Gnomad4 OTH AF: 0.00630

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 23, 2019

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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;