chr2-96551095-C-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_212481.3(ARID5A):c.571-4C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000645 in 1,605,886 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_212481.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID5A | NM_212481.3 | c.571-4C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000357485.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID5A | ENST00000357485.8 | c.571-4C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_212481.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 65AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000413 AC: 101AN: 244836Hom.: 0 AF XY: 0.000415 AC XY: 55AN XY: 132636
GnomAD4 exome AF: 0.000668 AC: 971AN: 1453608Hom.: 1 Cov.: 31 AF XY: 0.000637 AC XY: 460AN XY: 722470
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74446
ClinVar
Submissions by phenotype
ARID5A-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 13, 2024 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at