chr12-103994469-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001384711.1(GLT8D2):c.633G>C(p.Lys211Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000123 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K211E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001384711.1 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 |
---|---|---|---|---|---|---|---|
GLT8D2 | NM_001384711.1 | c.633G>C | p.Lys211Asn | missense_variant | 9/11 | ENST00000360814.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000360814.9 | c.633G>C | p.Lys211Asn | missense_variant | 9/11 | 1 | NM_001384711.1 | P1 | |
GLT8D2 | ENST00000546436.5 | c.633G>C | p.Lys211Asn | missense_variant | 8/10 | 5 | P1 | ||
GLT8D2 | ENST00000548660.5 | c.633G>C | p.Lys211Asn | missense_variant | 9/11 | 2 | P1 | ||
GLT8D2 | ENST00000552572.1 | n.145G>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250676Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135530
GnomAD4 exome AF: 0.000132 AC: 193AN: 1461746Hom.: 0 Cov.: 30 AF XY: 0.000124 AC XY: 90AN XY: 727166
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.633G>C (p.K211N) alteration is located in exon 9 (coding exon 7) of the GLT8D2 gene. This alteration results from a G to C substitution at nucleotide position 633, causing the lysine (K) at amino acid position 211 to be replaced by an asparagine (N). 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