rs1255831719

Variant names:

• chr1-63370753-CT-C
• rs1255831719
• NM_013339.4:c.-207-9delT

Your query was ambiguous. Multiple possible variants found:

• chr1-63370753-CT-C
• chr1-63370753-CT-CTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013339.4(ALG6):​c.-207-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000459 in 549,548 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00063 (0 hom.)
• Consequence: ALG6 NM_013339.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283

Genes affected

ALG6 (HGNC:23157): (ALG6 alpha-1,3-glucosyltransferase) This gene encodes a member of the ALG6/ALG8 glucosyltransferase family. The encoded protein catalyzes the addition of the first glucose residue to the growing lipid-linked oligosaccharide precursor of N-linked glycosylation. Mutations in this gene are associated with congenital disorders of glycosylation type Ic. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ALG6	NM_013339.4	c.-207-9delT		intron_variant	Intron 1 of 14	ENST00000263440.6	NP_037471.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ALG6	ENST00000263440.6	c.-207-17delT		intron_variant	Intron 1 of 14	5	NM_013339.4	ENSP00000263440.5

Frequencies

GnomAD3 genomes AF: 0.00000661 AC: 1 AN: 151326 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000630 AC: 251 AN: 398222 Hom.: 0 Cov.: 0 AF XY: 0.000582 AC XY: 124 AN XY: 213090

Gnomad4 AFR exome AF: 0.000358

Gnomad4 AMR exome AF: 0.000879

Gnomad4 ASJ exome AF: 0.000679

Gnomad4 EAS exome AF: 0.000726

Gnomad4 SAS exome AF: 0.000273

Gnomad4 FIN exome AF: 0.000630

Gnomad4 NFE exome AF: 0.000692

Gnomad4 OTH exome AF: 0.000530

GnomAD4 genome AF: 0.00000661 AC: 1 AN: 151326 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 73922

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1255831719; hg19: chr1-63836424;