1-203683266-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001684.5(ATP2B4):c.61G>A(p.Asp21Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000958 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D21A) has been classified as Uncertain significance.
Frequency
Consequence
NM_001684.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP2B4 | NM_001684.5 | c.61G>A | p.Asp21Asn | missense_variant | 2/21 | ENST00000357681.10 | |
ATP2B4 | NM_001001396.3 | c.61G>A | p.Asp21Asn | missense_variant | 2/22 | ||
ATP2B4 | NM_001365783.2 | c.61G>A | p.Asp21Asn | missense_variant | 2/21 | ||
ATP2B4 | NM_001365784.2 | c.61G>A | p.Asp21Asn | missense_variant | 2/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP2B4 | ENST00000357681.10 | c.61G>A | p.Asp21Asn | missense_variant | 2/21 | 1 | NM_001684.5 | A1 | |
ATP2B4 | ENST00000341360.7 | c.61G>A | p.Asp21Asn | missense_variant | 2/22 | 1 | P4 | ||
ATP2B4 | ENST00000705901.1 | c.61G>A | p.Asp21Asn | missense_variant | 2/21 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461892Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 727248
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.61G>A (p.D21N) alteration is located in exon 2 (coding exon 1) of the ATP2B4 gene. This alteration results from a G to A substitution at nucleotide position 61, causing the aspartic acid (D) at amino acid position 21 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at