chr7-135034379-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_178563.4(AGBL3):c.788T>G(p.Ile263Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000715 in 1,399,360 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.1e-7 ( 0 hom. )
Consequence
AGBL3
NM_178563.4 missense
NM_178563.4 missense
Scores
5
9
3
Clinical Significance
Conservation
PhyloP100: 7.55
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL3 | NM_178563.4 | c.788T>G | p.Ile263Ser | missense_variant | 7/17 | ENST00000436302.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL3 | ENST00000436302.6 | c.788T>G | p.Ile263Ser | missense_variant | 7/17 | 2 | NM_178563.4 | P2 | |
AGBL3 | ENST00000275763.10 | c.788T>G | p.Ile263Ser | missense_variant, NMD_transcript_variant | 7/17 | 1 | |||
AGBL3 | ENST00000435976.6 | c.788T>G | p.Ile263Ser | missense_variant | 7/16 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 7.15e-7 AC: 1AN: 1399360Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 690180
GnomAD4 exome
AF:
AC:
1
AN:
1399360
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
690180
Gnomad4 AFR exome
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Gnomad4 EAS exome
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Gnomad4 FIN exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 25, 2023 | The c.788T>G (p.I263S) alteration is located in exon 7 (coding exon 6) of the AGBL3 gene. This alteration results from a T to G substitution at nucleotide position 788, causing the isoleucine (I) at amino acid position 263 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
H;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
P;.
Vest4
MutPred
Gain of disorder (P = 0.0042);Gain of disorder (P = 0.0042);
MVP
ClinPred
D
GERP RS
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.