15-34857070-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM2PP2BP4_StrongBP6_Moderate
The NM_014691.3(AQR):c.4180G>A(p.Gly1394Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000312 in 1,604,856 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 Likely benign (★).
Frequency
Consequence
NM_014691.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AQR | NM_014691.3 | c.4180G>A | p.Gly1394Ser | missense_variant | 35/35 | ENST00000156471.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AQR | ENST00000156471.10 | c.4180G>A | p.Gly1394Ser | missense_variant | 35/35 | 1 | NM_014691.3 | P1 | |
AQR | ENST00000559090.5 | n.3067G>A | non_coding_transcript_exon_variant | 4/4 | 1 | ||||
AQR | ENST00000559767.1 | n.509G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
AQR | ENST00000543879.6 | c.*2942G>A | 3_prime_UTR_variant, NMD_transcript_variant | 34/34 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151852Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000124 AC: 3AN: 242400Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131446
GnomAD4 exome AF: 0.00000275 AC: 4AN: 1453004Hom.: 0 Cov.: 40 AF XY: 0.00000277 AC XY: 2AN XY: 722308
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151852Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74162
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at