chr7-134993499-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_178563.4(AGBL3):c.131C>G(p.Ser44Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000485 in 1,544,608 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_178563.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL3 | NM_178563.4 | c.131C>G | p.Ser44Cys | missense_variant | 4/17 | ENST00000436302.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL3 | ENST00000436302.6 | c.131C>G | p.Ser44Cys | missense_variant | 4/17 | 2 | NM_178563.4 | P2 | |
ENST00000665703.1 | n.71+4584G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00224 AC: 340AN: 151798Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000523 AC: 79AN: 151092Hom.: 1 AF XY: 0.000376 AC XY: 30AN XY: 79746
GnomAD4 exome AF: 0.000285 AC: 397AN: 1392692Hom.: 3 Cov.: 29 AF XY: 0.000272 AC XY: 187AN XY: 686306
GnomAD4 genome ? AF: 0.00232 AC: 352AN: 151916Hom.: 1 Cov.: 32 AF XY: 0.00225 AC XY: 167AN XY: 74260
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at