Variant chr22-49903386-CCT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_024105.4(ALG12):c.*450_*451del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0949 in 457,934 control chromosomes in the GnomAD database, including 2,402 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.078 ( 583 hom., cov: 31)

Exomes 𝑓: 0.10 ( 1819 hom. )

Consequence

ALG12
NM_024105.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.268

Variant links:

Genes affected

ALG12 (HGNC:19358): (ALG12 alpha-1,6-mannosyltransferase) This gene encodes a member of the glycosyltransferase 22 family. The encoded protein catalyzes the addition of the eighth mannose residue in an alpha-1,6 linkage onto the dolichol-PP-oligosaccharide precursor (dolichol-PP-Man(7)GlcNAc(2)) required for protein glycosylation. Mutations in this gene have been associated with congenital disorder of glycosylation type Ig (CDG-Ig)characterized by abnormal N-glycosylation. [provided by RefSeq, Jul 2008]

ALG12 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 22-49903386-CCT-C is Benign according to our data. Variant chr22-49903386-CCT-C is described in ClinVar as [Likely_benign]. Clinvar id is 342032.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
ALG12	NM_024105.4 linkuse as main transcript	c.450_451del	3_prime_UTR_variant	10/10	ENST00000330817.11	NP_077010.1
ALG12	XM_017028936.2 linkuse as main transcript	c.1238+791_1238+792del	intron_variant			XP_016884425.1
ALG12	XM_017028937.2 linkuse as main transcript	c.1238+791_1238+792del	intron_variant			XP_016884426.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALG12	ENST00000330817.11 linkuse as main transcript	c.450_451del		3_prime_UTR_variant	10/10	1	NM_024105.4	ENSP00000333813	P1
	ENST00000610245.1 linkuse as main transcript	n.1160_1161del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.0785

AC:

11949

AN:

152140

Hom.:

583

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0186

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.0793

Gnomad ASJ

AF:

0.0914

Gnomad EAS

AF:

0.0416

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.0664

GnomAD3 exomes

AF:

0.0925

AC:

12704

AN:

137288

Hom.:

648

AF XY:

0.0967

AC XY:

7196

AN XY:

74424

show subpopulations

Gnomad AFR exome

AF:

0.0152

Gnomad AMR exome

AF:

0.0682

Gnomad ASJ exome

AF:

0.101

Gnomad EAS exome

AF:

0.0340

Gnomad SAS exome

AF:

0.129

Gnomad FIN exome

AF:

0.112

Gnomad NFE exome

AF:

0.106

Gnomad OTH exome

AF:

0.0870

GnomAD4 exome

AF:

0.103

AC:

31496

AN:

305678

Hom.:

1819

AF XY:

0.107

AC XY:

18633

AN XY:

173992

show subpopulations

Gnomad4 AFR exome

AF:

0.0182

Gnomad4 AMR exome

AF:

0.0656

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.0363

Gnomad4 SAS exome

AF:

0.128

Gnomad4 FIN exome

AF:

0.110

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.0937

GnomAD4 genome

AF:

0.0785

AC:

11950

AN:

152256

Hom.:

583

Cov.:

AF XY:

0.0781

AC XY:

5812

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.0186

Gnomad4 AMR

AF:

0.0794

Gnomad4 ASJ

AF:

0.0914

Gnomad4 EAS

AF:

0.0413

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.113

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.0657

Alfa

AF:

0.0980

Hom.:

153

Bravo

AF:

0.0704

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Congenital disorder of glycosylation

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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