5-160602671-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025153.3(ATP10B):c.3269G>A(p.Arg1090His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025153.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP10B | NM_025153.3 | c.3269G>A | p.Arg1090His | missense_variant | 21/26 | ENST00000327245.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP10B | ENST00000327245.10 | c.3269G>A | p.Arg1090His | missense_variant | 21/26 | 1 | NM_025153.3 | P1 | |
ATP10B | ENST00000642502.1 | c.3185G>A | p.Arg1062His | missense_variant | 16/21 | ||||
ATP10B | ENST00000523758.1 | n.435G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 249028Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135064
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461648Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 727134
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 07, 2023 | The c.3269G>A (p.R1090H) alteration is located in exon 21 (coding exon 17) of the ATP10B gene. This alteration results from a G to A substitution at nucleotide position 3269, causing the arginine (R) at amino acid position 1090 to be replaced by a histidine (H). 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