5-138763637-C-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001903.5(CTNNA1):c.-3+10127C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00023 in 152,298 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 (no stars).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Consequence
CTNNA1
NM_001903.5 intron
NM_001903.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.236
Genes affected
CTNNA1 (HGNC:2509): (catenin alpha 1) This gene encodes a member of the catenin family of proteins that play an important role in cell adhesion process by connecting cadherins located on the plasma membrane to the actin filaments inside the cell. The encoded mechanosensing protein contains three vinculin homology domains and undergoes conformational changes in response to cytoskeletal tension, resulting in the reconfiguration of cadherin-actin filament connections. Certain mutations in this gene cause butterfly-shaped pigment dystrophy. [provided by RefSeq, May 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.66).
BP6
Variant 5-138763637-C-G is Benign according to our data. Variant chr5-138763637-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 223781.Status of the report is no_assertion_criteria_provided, 0 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00023 (35/152298) while in subpopulation SAS AF= 0.00538 (26/4834). AF 95% confidence interval is 0.00377. There are 0 homozygotes in gnomad4. There are 18 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 35 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CTNNA1 | NM_001903.5 | c.-3+10127C>G | intron_variant | Intron 1 of 17 | ENST00000302763.12 | NP_001894.2 |
Ensembl
Frequencies
GnomAD3 genomes 0.000230 AC: 35AN: 152180Hom.: 0 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.000230 AC: 35AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000242 AC XY: 18AN XY: 74458
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:1
Dec 01, 2015
University of Washington Department of Laboratory Medicine, University of Washington
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing
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Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at