chr2-215319657-T-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004044.7(ATIC):c.224-8T>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 0.00045 in 1,603,986 control chromosomes in the GnomAD database, including 4 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 Benign (★★).
Frequency
Consequence
NM_004044.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATIC | NM_004044.7 | c.224-8T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000236959.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATIC | ENST00000236959.14 | c.224-8T>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004044.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 288AN: 152212Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000613 AC: 154AN: 251168Hom.: 0 AF XY: 0.000442 AC XY: 60AN XY: 135798
GnomAD4 exome AF: 0.000298 AC: 432AN: 1451656Hom.: 2 Cov.: 30 AF XY: 0.000248 AC XY: 179AN XY: 723008
GnomAD4 genome AF: 0.00190 AC: 290AN: 152330Hom.: 2 Cov.: 32 AF XY: 0.00184 AC XY: 137AN XY: 74502
ClinVar
Submissions by phenotype
ATIC-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 22, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at