rs10638303

Positions:

• chr6-87508882-C-CCACT

Variant summary

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

The NM_006416.5(SLC35A1):​c.752-157_752-156insCTCA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.39 (11337 hom., cov: 0)
• Consequence: SLC35A1 NM_006416.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1 O:1
• Conservation: PhyloP100: -1.51

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 6-87508882-C-CCACT is Benign according to our data. Variant chr6-87508882-C-CCACT is described in ClinVar as [Benign]. Clinvar id is 4843.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.454 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC35A1	NM_006416.5	c.752-157_752-156insCTCA		intron_variant		ENST00000369552.9
SLC35A1	NM_001168398.2	c.575-157_575-156insCTCA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC35A1	ENST00000369552.9	c.752-157_752-156insCTCA		intron_variant		1	NM_006416.5	P1
SLC35A1	ENST00000369556.7	c.575-157_575-156insCTCA		intron_variant		1
SLC35A1	ENST00000369557.9	c.508-157_508-156insCTCA		intron_variant		2
SLC35A1	ENST00000464978.5	n.760-157_760-156insCTCA		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58500 AN: 151578 Hom.: 11323 Cov.: 0

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.386 AC: 58534 AN: 151696 Hom.: 11337 Cov.: 0 AF XY: 0.384 AC XY: 28448 AN XY: 74120

Gnomad4 AFR AF: 0.434

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.380

Alfa AF: 0.378 Hom.: 1266

Bravo AF: 0.400

Asia WGS AF: 0.344 AC: 1196 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IIf, MODIFIER OF Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Apr 01, 2005

- -

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: rs10638303; hg19: chr6-88218600;