18-12366987-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_006796.3(AFG3L2):āc.530A>Gā(p.Asn177Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,614,124 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N177D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006796.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AFG3L2 | NM_006796.3 | c.530A>G | p.Asn177Ser | missense_variant | 5/17 | ENST00000269143.8 | |
AFG3L2 | XM_011525601.4 | c.530A>G | p.Asn177Ser | missense_variant | 5/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AFG3L2 | ENST00000269143.8 | c.530A>G | p.Asn177Ser | missense_variant | 5/17 | 1 | NM_006796.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251482Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135912
GnomAD4 exome AF: 0.000119 AC: 174AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.000105 AC XY: 76AN XY: 727248
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 21, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Nov 24, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at