chrX-153541663-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001001344.3(ATP2B3):c.407-6G>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 0.00278 in 1,208,161 control chromosomes in the GnomAD database, including 67 homozygotes. There are 851 hemizygotes in GnomAD. 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_001001344.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B3 | NM_001001344.3 | c.407-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000263519.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B3 | ENST00000263519.5 | c.407-6G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001001344.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0147 AC: 1636AN: 111520Hom.: 36 Cov.: 23 AF XY: 0.0123 AC XY: 414AN XY: 33720
GnomAD3 exomes AF: 0.00415 AC: 755AN: 182076Hom.: 14 AF XY: 0.00253 AC XY: 169AN XY: 66770
GnomAD4 exome AF: 0.00156 AC: 1714AN: 1096587Hom.: 31 Cov.: 32 AF XY: 0.00119 AC XY: 432AN XY: 362259
GnomAD4 genome AF: 0.0147 AC: 1645AN: 111574Hom.: 36 Cov.: 23 AF XY: 0.0124 AC XY: 419AN XY: 33784
ClinVar
Submissions by phenotype
X-linked progressive cerebellar ataxia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 11, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at