rs7159558

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000261534.9(POMT2):​c.*790G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,182 control chromosomes in the GnomAD database, including 23,969 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 23961 hom., cov: 33)
Exomes 𝑓: 0.44 ( 8 hom. )

Consequence

POMT2
ENST00000261534.9 3_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: 0.211
Variant links:
Genes affected
POMT2 (HGNC:19743): (protein O-mannosyltransferase 2) The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT1 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).[provided by RefSeq, Oct 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant 14-77276586-C-T is Benign according to our data. Variant chr14-77276586-C-T is described in ClinVar as [Benign]. Clinvar id is 314536.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
POMT2NM_013382.7 linkuse as main transcriptc.*790G>A 3_prime_UTR_variant 21/21 ENST00000261534.9 NP_037514.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
POMT2ENST00000261534.9 linkuse as main transcriptc.*790G>A 3_prime_UTR_variant 21/211 NM_013382.7 ENSP00000261534 P1Q9UKY4-1

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84474
AN:
151980
Hom.:
23940
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.601
Gnomad AMI
AF:
0.557
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.444
Gnomad SAS
AF:
0.453
Gnomad FIN
AF:
0.638
Gnomad MID
AF:
0.491
Gnomad NFE
AF:
0.567
Gnomad OTH
AF:
0.533
GnomAD4 exome
AF:
0.439
AC:
36
AN:
82
Hom.:
8
Cov.:
0
AF XY:
0.357
AC XY:
20
AN XY:
56
show subpopulations
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.688
Gnomad4 NFE exome
AF:
0.380
Gnomad4 OTH exome
AF:
0.625
GnomAD4 genome
AF:
0.556
AC:
84528
AN:
152100
Hom.:
23961
Cov.:
33
AF XY:
0.554
AC XY:
41178
AN XY:
74380
show subpopulations
Gnomad4 AFR
AF:
0.601
Gnomad4 AMR
AF:
0.410
Gnomad4 ASJ
AF:
0.504
Gnomad4 EAS
AF:
0.445
Gnomad4 SAS
AF:
0.453
Gnomad4 FIN
AF:
0.638
Gnomad4 NFE
AF:
0.567
Gnomad4 OTH
AF:
0.538
Alfa
AF:
0.550
Hom.:
22164
Bravo
AF:
0.540
Asia WGS
AF:
0.486
AC:
1688
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2N Benign:1
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
4.0
DANN
Benign
0.44

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.

Other links and lift over

dbSNP: rs7159558; hg19: chr14-77742929; API