chr15-89908322-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_182616.4(ARPIN):c.259G>A(p.Ala87Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182616.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARPIN | NM_182616.4 | c.259G>A | p.Ala87Thr | missense_variant | 3/6 | ENST00000357484.10 | |
ARPIN-AP3S2 | NM_001199058.2 | c.259G>A | p.Ala87Thr | missense_variant | 3/10 | ||
ARPIN | NM_001282380.2 | c.-30G>A | 5_prime_UTR_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARPIN | ENST00000357484.10 | c.259G>A | p.Ala87Thr | missense_variant | 3/6 | 1 | NM_182616.4 | P1 | |
ARPIN | ENST00000460685.1 | c.-30G>A | 5_prime_UTR_variant | 3/6 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249502Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135380
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461882Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727242
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.259G>A (p.A87T) alteration is located in exon 3 (coding exon 3) of the ARPIN gene. This alteration results from a G to A substitution at nucleotide position 259, causing the alanine (A) at amino acid position 87 to be replaced by a threonine (T). 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