chr12-109855686-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_016433.4(GLTP):āc.380A>Gā(p.Asn127Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,608,272 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. N127N) has been classified as Benign.
Frequency
Consequence
NM_016433.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLTP | NM_016433.4 | c.380A>G | p.Asn127Ser | missense_variant | 4/5 | ENST00000318348.9 | |
GLTP | XM_047428937.1 | c.257A>G | p.Asn86Ser | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLTP | ENST00000318348.9 | c.380A>G | p.Asn127Ser | missense_variant | 4/5 | 1 | NM_016433.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150582Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248150Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134336
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457690Hom.: 0 Cov.: 31 AF XY: 0.00000689 AC XY: 5AN XY: 725370
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150582Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 23, 2023 | The c.380A>G (p.N127S) alteration is located in exon 4 (coding exon 4) of the GLTP gene. This alteration results from a A to G substitution at nucleotide position 380, causing the asparagine (N) at amino acid position 127 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