2-79523465-G-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001282597.3(CTNNA2):c.-6+10258G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,994 control chromosomes in the GnomAD database, including 32,906 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.66 ( 32906 hom., cov: 33)
Consequence
CTNNA2
NM_001282597.3 intron
NM_001282597.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
Genes affected
CTNNA2 (HGNC:2510): (catenin alpha 2) Enables actin filament binding activity. Involved in negative regulation of Arp2/3 complex-mediated actin nucleation; regulation of neuron migration; and regulation of neuron projection development. Located in cytoplasm. Implicated in complex cortical dysplasia with other brain malformations. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 2-79523465-G-T is Benign according to our data. Variant chr2-79523465-G-T is described in ClinVar as [Benign]. Clinvar id is 1249105.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNA2 | NM_001282597.3 | c.-6+10258G>T | intron_variant | ENST00000402739.9 | NP_001269526.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTNNA2 | ENST00000402739.9 | c.-6+10258G>T | intron_variant | 1 | NM_001282597.3 | ENSP00000384638.4 |
Frequencies
GnomAD3 genomes AF: 0.657 AC: 99812AN: 151878Hom.: 32878 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.657 AC: 99887AN: 151994Hom.: 32906 Cov.: 33 AF XY: 0.655 AC XY: 48673AN XY: 74294
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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 | May 11, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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