6-49521743-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010904.2(GLYATL3):c.412G>A(p.Val138Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000451 in 1,551,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010904.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLYATL3 | NM_001010904.2 | c.412G>A | p.Val138Ile | missense_variant | 5/6 | ENST00000371197.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLYATL3 | ENST00000371197.9 | c.412G>A | p.Val138Ile | missense_variant | 5/6 | 2 | NM_001010904.2 | P1 | |
GLYATL3 | ENST00000545705.1 | c.412G>A | p.Val138Ile | missense_variant | 5/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 153824Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 81618
GnomAD4 exome AF: 0.00000357 AC: 5AN: 1399166Hom.: 0 Cov.: 31 AF XY: 0.00000290 AC XY: 2AN XY: 690074
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at