chr2-209817086-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001371986.1(UNC80):c.1513C>A(p.Arg505Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,399,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
UNC80
NM_001371986.1 synonymous
NM_001371986.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.49
Publications
1 publications found
Genes affected
UNC80 (HGNC:26582): (unc-80 homolog, NALCN channel complex subunit) The protein encoded by this gene is a component of a voltage-independent 'leak' ion-channel complex, in which it performs essential functions, such as serving as a bridge between two other components (sodium leak channel non-selective and UNC79) and as a scaffold for Src kinases. Leak channels play an importnat role in establishment and maintenance of resting membrane potentials in neurons. Mutations in this gene are associated with congenital infantile encephalopathy, intellectual disability and growth issues. [provided by RefSeq, Aug 2016]
UNC80 Gene-Disease associations (from GenCC):
- hypotonia, infantile, with psychomotor retardation and characteristic facies 2Inheritance: AR, AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Illumina, ClinGen
- hypotonia, infantile, with psychomotor retardation and characteristic faciesInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.19).
BP6
Variant 2-209817086-C-A is Benign according to our data. Variant chr2-209817086-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2024339.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.49 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
UNC80 | NM_001371986.1 | c.1513C>A | p.Arg505Arg | synonymous_variant | Exon 10 of 65 | ENST00000673920.1 | NP_001358915.1 | |
UNC80 | NM_032504.2 | c.1513C>A | p.Arg505Arg | synonymous_variant | Exon 10 of 64 | NP_115893.1 | ||
UNC80 | NM_182587.4 | c.1513C>A | p.Arg505Arg | synonymous_variant | Exon 10 of 63 | NP_872393.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
UNC80 | ENST00000673920.1 | c.1513C>A | p.Arg505Arg | synonymous_variant | Exon 10 of 65 | NM_001371986.1 | ENSP00000501211.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000637 AC: 1AN: 157044 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
157044
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000143 AC: 20AN: 1399474Hom.: 0 Cov.: 30 AF XY: 0.0000130 AC XY: 9AN XY: 690238 show subpopulations
GnomAD4 exome
AF:
AC:
20
AN:
1399474
Hom.:
Cov.:
30
AF XY:
AC XY:
9
AN XY:
690238
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31598
American (AMR)
AF:
AC:
0
AN:
35704
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25182
East Asian (EAS)
AF:
AC:
0
AN:
35738
South Asian (SAS)
AF:
AC:
0
AN:
79234
European-Finnish (FIN)
AF:
AC:
0
AN:
49320
Middle Eastern (MID)
AF:
AC:
0
AN:
5674
European-Non Finnish (NFE)
AF:
AC:
19
AN:
1078990
Other (OTH)
AF:
AC:
1
AN:
58034
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.453
Heterozygous variant carriers
0
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0.00
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Sep 04, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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