Variant 12-34026222-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000266483.7(ALG10):c.729C>T(p.Ser243=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00621 in 1,613,954 control chromosomes in the GnomAD database, including 382 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.028 ( 183 hom., cov: 32)

Exomes 𝑓: 0.0040 ( 199 hom. )

Consequence

ALG10
ENST00000266483.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.856

Variant links:

Genes affected

ALG10 (HGNC:23162): (ALG10 alpha-1,2-glucosyltransferase) This gene encodes a membrane-associated protein that adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. That is, it transfers the terminal glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc2Man9GlcNAc(2)-PP-Dol. The rat protein homolog was shown to specifically modulate the gating function of the rat neuronal ether-a-go-go (EAG) potassium ion channel. [provided by RefSeq, Jan 2010]

ALG10 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 12-34026222-C-T is Benign according to our data. Variant chr12-34026222-C-T is described in ClinVar as [Benign]. Clinvar id is 776699.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.856 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
ALG10	NM_032834.4 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	3/3	ENST00000266483.7	NP_116223.3
ALG10	XM_024449230.2 linkuse as main transcript	c.549C>T	p.Ser183=	synonymous_variant	3/3		XP_024304998.1
ALG10	XM_024449231.2 linkuse as main transcript	c.549C>T	p.Ser183=	synonymous_variant	3/3		XP_024304999.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris
ALG10	ENST00000266483.7 linkuse as main transcript	c.729C>T	p.Ser243=	synonymous_variant	3/3	1	NM_032834.4	ENSP00000266483	P1
ALG10	ENST00000541875.1 linkuse as main transcript	c.*469C>T		3_prime_UTR_variant, NMD_transcript_variant	3/3	1		ENSP00000443142
	ENST00000501954.2 linkuse as main transcript	n.326-2088G>A		intron_variant, non_coding_transcript_variant		5
ALG10	ENST00000538927.1 linkuse as main transcript	c.369+2063C>T		intron_variant		5		ENSP00000444084

Frequencies

GnomAD3 genomes

AF:

0.0277

AC:

4208

AN:

152046

Hom.:

181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0891

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0207

Gnomad ASJ

AF:

0.00722

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00185

Gnomad OTH

AF:

0.0230

GnomAD3 exomes

AF:

0.00870

AC:

2186

AN:

251314

Hom.:

AF XY:

0.00666

AC XY:

904

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.0944

Gnomad AMR exome

AF:

0.00977

Gnomad ASJ exome

AF:

0.00585

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000392

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00175

Gnomad OTH exome

AF:

0.00718

GnomAD4 exome

AF:

0.00396

AC:

5796

AN:

1461790

Hom.:

199

Cov.:

AF XY:

0.00362

AC XY:

2633

AN XY:

727198

show subpopulations

Gnomad4 AFR exome

AF:

0.0980

Gnomad4 AMR exome

AF:

0.0105

Gnomad4 ASJ exome

AF:

0.00520

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000336

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00111

Gnomad4 OTH exome

AF:

0.00947

GnomAD4 genome

AF:

0.0278

AC:

4233

AN:

152164

Hom.:

183

Cov.:

AF XY:

0.0267

AC XY:

1986

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.0895

Gnomad4 AMR

AF:

0.0206

Gnomad4 ASJ

AF:

0.00722

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00184

Gnomad4 OTH

AF:

0.0228

Alfa

AF:

0.0124

Hom.:

Bravo

AF:

0.0322

Asia WGS

AF:

0.00779

AC:

AN:

3478

EpiCase

AF:

0.00164

EpiControl

AF:

0.00267

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

3.8

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over