rs4305737
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_007124.3(UTRN):c.7911G>A(p.Glu2637=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 1,607,788 control chromosomes in the GnomAD database, including 106,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.46 ( 21177 hom., cov: 32)
Exomes 𝑓: 0.30 ( 84902 hom. )
Consequence
UTRN
NM_007124.3 synonymous
NM_007124.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.07
Genes affected
UTRN (HGNC:12635): (utrophin) This gene shares both structural and functional similarities with the dystrophin gene. It contains an actin-binding N-terminus, a triple coiled-coil repeat central region, and a C-terminus that consists of protein-protein interaction motifs which interact with dystroglycan protein components. The protein encoded by this gene is located at the neuromuscular synapse and myotendinous junctions, where it participates in post-synaptic membrane maintenance and acetylcholine receptor clustering. Mouse studies suggest that this gene may serve as a functional substitute for the dystrophin gene and therefore, may serve as a potential therapeutic alternative to muscular dystrophy which is caused by mutations in the dystrophin gene. Alternative splicing of the utrophin gene has been described; however, the full-length nature of these variants has not yet been determined. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
?
Variant 6-144730458-G-A is Benign according to our data. Variant chr6-144730458-G-A is described in ClinVar as [Benign]. Clinvar id is 1266647.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.07 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTRN | NM_007124.3 | c.7911G>A | p.Glu2637= | synonymous_variant | 54/75 | ENST00000367545.8 | |
UTRN | NM_001375323.1 | c.576G>A | p.Glu192= | synonymous_variant | 4/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTRN | ENST00000367545.8 | c.7911G>A | p.Glu2637= | synonymous_variant | 54/75 | 5 | NM_007124.3 | P1 | |
UTRN | ENST00000367526.8 | c.576G>A | p.Glu192= | synonymous_variant | 4/25 | 5 | |||
UTRN | ENST00000367524.8 | c.576G>A | p.Glu192= | synonymous_variant | 4/24 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.457 AC: 69474AN: 151866Hom.: 21114 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
69474
AN:
151866
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.415 AC: 102446AN: 246798Hom.: 28419 AF XY: 0.393 AC XY: 52621AN XY: 133738
GnomAD3 exomes
AF:
AC:
102446
AN:
246798
Hom.:
AF XY:
AC XY:
52621
AN XY:
133738
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.302 AC: 439169AN: 1455804Hom.: 84902 Cov.: 32 AF XY: 0.303 AC XY: 219196AN XY: 724358
GnomAD4 exome
AF:
AC:
439169
AN:
1455804
Hom.:
Cov.:
32
AF XY:
AC XY:
219196
AN XY:
724358
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.458 AC: 69600AN: 151984Hom.: 21177 Cov.: 32 AF XY: 0.461 AC XY: 34280AN XY: 74294
GnomAD4 genome
?
AF:
AC:
69600
AN:
151984
Hom.:
Cov.:
32
AF XY:
AC XY:
34280
AN XY:
74294
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2341
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at