9-131506458-AAG-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6BS2

The NM_001077365.2(POMT1):c.280+7_280+8delGA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000207 in 1,608,554 control chromosomes in the GnomAD database, including 5 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00011 ( 2 hom., cov: 32)

Exomes 𝑓: 0.00022 ( 3 hom. )

Consequence

POMT1
NM_001077365.2 splice_region, intron

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: -0.126

Publications

0 publications found

Variant links:

Genes affected

POMT1 (HGNC:9202): (protein O-mannosyltransferase 1) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT2 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS) and limb-girdle muscular dystrophy type 2K (LGMD2K). Several transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2008]

POMT1 Gene-Disease associations (from GenCC):

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Laboratory for Molecular Medicine, Genomics England PanelApp
myopathy caused by variation in POMT1
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
autosomal recessive limb-girdle muscular dystrophy type 2K
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
congenital muscular dystrophy with cerebellar involvement
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
congenital muscular dystrophy with intellectual disability
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
congenital muscular dystrophy without intellectual disability
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
muscle-eye-brain disease
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
muscular dystrophy-dystroglycanopathy, type A
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

POMT1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP6

Variant 9-131506458-AAG-A is Benign according to our data. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374. Variant chr9-131506458-AAG-A is described in CliVar as Conflicting_classifications_of_pathogenicity. Clinvar id is 436374.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POMT1	NM_001077365.2 link	c.280+7_280+8delGA		splice_region_variant, intron_variant	Intron 4 of 19	ENST00000402686.8	NP_001070833.1	Q9Y6A1-2A0A140VKE0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POMT1	ENST00000402686.8 link	c.280+7_280+8delGA		splice_region_variant, intron_variant	Intron 4 of 19	1	NM_001077365.2	ENSP00000385797.4		Q9Y6A1-2

Frequencies

GnomAD3 genomes

AF:

0.000112

AC:

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00353

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000489

AC:

123

AN:

251472

AF XY:

0.000589

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000163

GnomAD4 exome

AF:

0.000217

AC:

316

AN:

1456226

Hom.:

AF XY:

0.000295

AC XY:

214

AN XY:

724824

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33342

American (AMR)

AF:

0.00

AC:

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26112

East Asian (EAS)

AF:

0.00

AC:

AN:

39646

South Asian (SAS)

AF:

0.00343

AC:

295

AN:

86110

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.000521

AC:

AN:

5756

European-Non Finnish (NFE)

AF:

0.00000181

AC:

AN:

1106904

Other (OTH)

AF:

0.000266

AC:

AN:

60222

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.449

Heterozygous variant carriers

107

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000112

AC:

AN:

152328

Hom.:

Cov.:

AF XY:

0.000215

AC XY:

AN XY:

74488

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41558

American (AMR)

AF:

0.00

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00353

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

68036

Other (OTH)

AF:

0.00

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.529

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0000434

Hom.:

Bravo

AF:

0.0000227

Asia WGS

AF:

0.000577

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1Benign:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Sep 13, 2016

Genetic Services Laboratory, University of Chicago

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Walker-Warburg congenital muscular dystrophy;C1836373:Autosomal recessive limb-girdle muscular dystrophy type 2K;C5436962:Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1

Benign:1

Nov 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.13

Mutation Taster

=100/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over