chr9-135626142-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_182974.3(GLT6D1):c.184G>A(p.Asp62Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,614,052 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182974.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT6D1 | NM_182974.3 | c.184G>A | p.Asp62Asn | missense_variant | 4/5 | ENST00000371763.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT6D1 | ENST00000371763.6 | c.184G>A | p.Asp62Asn | missense_variant | 4/5 | 1 | NM_182974.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249542Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135390
GnomAD4 exome AF: 0.000129 AC: 189AN: 1461744Hom.: 2 Cov.: 32 AF XY: 0.000136 AC XY: 99AN XY: 727172
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000107 AC XY: 8AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2022 | The c.184G>A (p.D62N) alteration is located in exon 4 (coding exon 3) of the GLT6D1 gene. This alteration results from a G to A substitution at nucleotide position 184, causing the aspartic acid (D) at amino acid position 62 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