chr12-128875945-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_144669.3(GLT1D1):c.100G>A(p.Val34Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000751 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 Likely benign (★).
Frequency
Consequence
NM_144669.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLT1D1 | NM_001366886.1 | c.100G>A | p.Val34Ile | missense_variant | 2/12 | ENST00000442111.7 | |
GLT1D1 | NR_159493.1 | n.204G>A | non_coding_transcript_exon_variant | 2/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLT1D1 | ENST00000442111.7 | c.100G>A | p.Val34Ile | missense_variant | 2/12 | 5 | NM_001366886.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000618 AC: 94AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000290 AC: 73AN: 251390Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135880
GnomAD4 exome AF: 0.000766 AC: 1119AN: 1461774Hom.: 2 Cov.: 31 AF XY: 0.000692 AC XY: 503AN XY: 727198
GnomAD4 genome ? AF: 0.000611 AC: 93AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74458
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at