rs369585470
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_170665.4(ATP2A2):c.545-7C>T 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 0.000174 in 1,613,210 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_170665.4 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 |
---|---|---|---|---|---|---|---|
ATP2A2 | NM_170665.4 | c.545-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000539276.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2A2 | ENST00000539276.7 | c.545-7C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_170665.4 | P3 |
Frequencies
GnomAD3 genomes AF: 0.000362 AC: 55AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000279 AC: 70AN: 250624Hom.: 0 AF XY: 0.000318 AC XY: 43AN XY: 135416
GnomAD4 exome AF: 0.000154 AC: 225AN: 1460980Hom.: 0 Cov.: 30 AF XY: 0.000160 AC XY: 116AN XY: 726734
GnomAD4 genome AF: 0.000361 AC: 55AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Dec 30, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 16, 2023 | - - |
Acrokeratosis verruciformis of Hopf Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Keratosis follicularis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Dec 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at