chr14-77275628-G-T

Variant summary

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

The NM_013382.7(POMT2):​c.*1748C>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 0.107 in 152,246 control chromosomes in the GnomAD database, including 1,804 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1804 hom., cov: 32)
Exomes 𝑓: 0.025 ( 0 hom. )

Consequence

POMT2
NM_013382.7 3_prime_UTR

Scores

2

Clinical Significance

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

Conservation

PhyloP100: -0.631
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=-0.85).
BP6
Variant 14-77275628-G-T is Benign according to our data. Variant chr14-77275628-G-T is described in ClinVar as [Benign]. Clinvar id is 314519.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
POMT2NM_013382.7 linkuse as main transcriptc.*1748C>A 3_prime_UTR_variant 21/21 ENST00000261534.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
POMT2ENST00000261534.9 linkuse as main transcriptc.*1748C>A 3_prime_UTR_variant 21/211 NM_013382.7 P1Q9UKY4-1

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16347
AN:
151968
Hom.:
1803
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.287
Gnomad AMI
AF:
0.0559
Gnomad AMR
AF:
0.0533
Gnomad ASJ
AF:
0.0479
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.0473
Gnomad FIN
AF:
0.0516
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0359
Gnomad OTH
AF:
0.102
GnomAD4 exome
AF:
0.0250
AC:
4
AN:
160
Hom.:
0
Cov.:
0
AF XY:
0.0364
AC XY:
4
AN XY:
110
show subpopulations
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0357
Gnomad4 NFE exome
AF:
0.0306
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.108
AC:
16359
AN:
152086
Hom.:
1804
Cov.:
32
AF XY:
0.105
AC XY:
7803
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.287
Gnomad4 AMR
AF:
0.0532
Gnomad4 ASJ
AF:
0.0479
Gnomad4 EAS
AF:
0.000387
Gnomad4 SAS
AF:
0.0469
Gnomad4 FIN
AF:
0.0516
Gnomad4 NFE
AF:
0.0359
Gnomad4 OTH
AF:
0.100
Alfa
AF:
0.0768
Hom.:
144
Bravo
AF:
0.117
Asia WGS
AF:
0.0380
AC:
131
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 12, 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
-0.85
CADD
Benign
0.82
DANN
Benign
0.58

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs45458096; hg19: chr14-77741971; API