chr1-48663230-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_032785.4(AGBL4):c.646G>A(p.Glu216Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00112 in 1,613,894 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032785.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL4 | NM_032785.4 | c.646G>A | p.Glu216Lys | missense_variant | 7/14 | ENST00000371839.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL4 | ENST00000371839.6 | c.646G>A | p.Glu216Lys | missense_variant | 7/14 | 2 | NM_032785.4 | P1 | |
AGBL4 | ENST00000416121.5 | c.184G>A | p.Glu62Lys | missense_variant | 3/7 | 1 | |||
AGBL4 | ENST00000371838.5 | c.646G>A | p.Glu216Lys | missense_variant | 7/9 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000624 AC: 95AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000425 AC: 106AN: 249220Hom.: 0 AF XY: 0.000481 AC XY: 65AN XY: 135198
GnomAD4 exome AF: 0.00118 AC: 1720AN: 1461650Hom.: 2 Cov.: 30 AF XY: 0.00111 AC XY: 806AN XY: 727106
GnomAD4 genome ? AF: 0.000624 AC: 95AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74454
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 16, 2021 | The c.646G>A (p.E216K) alteration is located in exon 7 (coding exon 7) of the AGBL4 gene. This alteration results from a G to A substitution at nucleotide position 646, causing the glutamic acid (E) at amino acid position 216 to be replaced by a lysine (K). 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