12-103994470-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001384711.1(GLT8D2):c.632A>G(p.Lys211Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000295 in 1,613,952 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT8D2 | NM_001384711.1 | c.632A>G | p.Lys211Arg | missense_variant | 9/11 | ENST00000360814.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT8D2 | ENST00000360814.9 | c.632A>G | p.Lys211Arg | missense_variant | 9/11 | 1 | NM_001384711.1 | P1 | |
GLT8D2 | ENST00000546436.5 | c.632A>G | p.Lys211Arg | missense_variant | 8/10 | 5 | P1 | ||
GLT8D2 | ENST00000548660.5 | c.632A>G | p.Lys211Arg | missense_variant | 9/11 | 2 | P1 | ||
GLT8D2 | ENST00000552572.1 | n.144A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000263 AC: 66AN: 250664Hom.: 2 AF XY: 0.000362 AC XY: 49AN XY: 135530
GnomAD4 exome AF: 0.000306 AC: 447AN: 1461752Hom.: 4 Cov.: 30 AF XY: 0.000337 AC XY: 245AN XY: 727168
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 21, 2021 | The c.632A>G (p.K211R) alteration is located in exon 9 (coding exon 7) of the GLT8D2 gene. This alteration results from a A to G substitution at nucleotide position 632, causing the lysine (K) at amino acid position 211 to be replaced by an arginine (R). 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