9-85547201-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001330701.2(AGTPBP1):c.3589A>G(p.Ile1197Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,752 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330701.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTPBP1 | NM_001330701.2 | c.3589A>G | p.Ile1197Val | missense_variant | 26/26 | ENST00000357081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTPBP1 | ENST00000357081.8 | c.3589A>G | p.Ile1197Val | missense_variant | 26/26 | 5 | NM_001330701.2 | P1 | |
AGTPBP1 | ENST00000376083.7 | c.3469A>G | p.Ile1157Val | missense_variant | 26/26 | 1 | |||
AGTPBP1 | ENST00000337006.8 | c.3745A>G | p.Ile1249Val | missense_variant | 25/25 | 5 | |||
AGTPBP1 | ENST00000628899.1 | c.3625A>G | p.Ile1209Val | missense_variant | 25/25 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 250918Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135656
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461506Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727090
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74372
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 02, 2024 | The c.3469A>G (p.I1157V) alteration is located in exon 26 (coding exon 25) of the AGTPBP1 gene. This alteration results from a A to G substitution at nucleotide position 3469, causing the isoleucine (I) at amino acid position 1157 to be replaced by a valine (V). 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