rs67504838

Variant names:

• chr11-45804038-TCC-T
• rs67504838
• ENST00000811651.1:n.43+1592_43+1593delGG

Your query was ambiguous. Multiple possible variants found:

• chr11-45804038-TCC-T
• chr11-45804038-TCC-TC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000811651.1(LINC02690):​n.43+1592_43+1593delGG 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: not found (cov: 0)
• Consequence: LINC02690 ENST00000811651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 1 publications found

Genes affected

LINC02690 (HGNC:54194): (long intergenic non-protein coding RNA 2690)

SLC35C1 (HGNC:20197): (solute carrier family 35 member C1) This gene encodes a GDP-fucose transporter that is found in the Golgi apparatus. Mutations in this gene result in congenital disorder of glycosylation type IIc. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

SLC35C1 Gene-Disease associations (from GenCC):

• leukocyte adhesion deficiency type II

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, PanelApp Australia

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811651.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC35C1	NM_001145266.2		c.-413_-412delCC		upstream_gene	N/A	NP_001138738.1	Q96A29-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02690	ENST00000811651.1		n.43+1592_43+1593delGG		intron	N/A
	SLC35C1	ENST00000442528.2	TSL:1	c.-510_-509delCC		upstream_gene	N/A	ENSP00000412408.2	Q96A29-2
	SLC35C1	ENST00000526817.2	TSL:2	c.-413_-412delCC		upstream_gene	N/A	ENSP00000432145.2	Q96A29-2

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs67504838; hg19: chr11-45825589;