15-86257970-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001386094.1(AGBL1):c.908T>C(p.Phe303Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,456 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001386094.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL1 | NM_001386094.1 | c.908T>C | p.Phe303Ser | missense_variant | 9/23 | ENST00000614907.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL1 | ENST00000614907.3 | c.908T>C | p.Phe303Ser | missense_variant | 9/23 | 5 | NM_001386094.1 | P4 | |
AGBL1 | ENST00000441037.7 | c.908T>C | p.Phe303Ser | missense_variant | 9/25 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000884 AC: 22AN: 248780Hom.: 0 AF XY: 0.0000889 AC XY: 12AN XY: 134956
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461270Hom.: 0 Cov.: 30 AF XY: 0.0000413 AC XY: 30AN XY: 726916
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.770T>C (p.F257S) alteration is located in exon 8 (coding exon 7) of the AGBL1 gene. This alteration results from a T to C substitution at nucleotide position 770, causing the phenylalanine (F) at amino acid position 257 to be replaced by a serine (S). 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