15-34856970-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_014691.3(AQR):c.4280G>A(p.Arg1427His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000743 in 1,614,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_014691.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQR | NM_014691.3 | c.4280G>A | p.Arg1427His | missense_variant | 35/35 | ENST00000156471.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQR | ENST00000156471.10 | c.4280G>A | p.Arg1427His | missense_variant | 35/35 | 1 | NM_014691.3 | P1 | |
AQR | ENST00000559090.5 | n.3167G>A | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
AQR | ENST00000559767.1 | n.609G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
AQR | ENST00000543879.6 | c.*3042G>A | 3_prime_UTR_variant, NMD_transcript_variant | 34/34 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152086Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249472Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135356
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1461874Hom.: 0 Cov.: 40 AF XY: 0.0000633 AC XY: 46AN XY: 727244
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74420
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.4280G>A (p.R1427H) alteration is located in exon 35 (coding exon 35) of the AQR gene. This alteration results from a G to A substitution at nucleotide position 4280, causing the arginine (R) at amino acid position 1427 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