Genetic Variant ALG10B:p.Ser25Phe (chr12-38316967-CC-TT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001013620.4(ALG10B):c.74_75delCCinsTT(p.Ser25Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S25C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

ALG10B
NM_001013620.4 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.04

Publications

0 publications found

Variant links:

Genes affected

ALG10B (HGNC:31088): (ALG10 alpha-1,2-glucosyltransferase B) Enables transferase activity. Involved in positive regulation of inward rectifier potassium channel activity; positive regulation of protein glycosylation; and protein glycosylation. Located in endoplasmic reticulum. Implicated in long QT syndrome 2. [provided by Alliance of Genome Resources, Apr 2022]

ALG10B Gene-Disease associations (from GenCC):

long QT syndrome
Inheritance: AD Classification: LIMITED Submitted by: ClinGen
long QT syndrome 2
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ALG10B links:

ENSG00000301992 (HGNC:):

ENSG00000301992 links:

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new If you want to explore the variant's impact on the transcript NM_001013620.4, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001013620.4. 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
	ALG10B	NM_001013620.4	MANE Select	c.74_75delCCinsTT	p.Ser25Phe	missense	N/A	NP_001013642.2	Q5I7T1
	ALG10B	NM_001308340.2		c.74_75delCCinsTT	p.Ser25Phe	missense	N/A	NP_001295269.2	F8VXJ0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ALG10B	ENST00000308742.9	TSL:1 MANE Select	c.74_75delCCinsTT	p.Ser25Phe	missense	N/A	ENSP00000310120.4	Q5I7T1
ALG10B	ENST00000548240.1	TSL:1	n.74_75delCCinsTT		non_coding_transcript_exon	Exon 1 of 3	ENSP00000449210.1	F8VWA9
ALG10B	ENST00000551464.1	TSL:3	c.74_75delCCinsTT	p.Ser25Phe	missense	N/A	ENSP00000448819.1	F8VXJ0

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

5.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over