3-37281997-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_002078.5(GOLGA4):c.202C>T(p.Arg68Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00111 in 1,614,028 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. R68Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_002078.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GOLGA4 | NM_002078.5 | c.202C>T | p.Arg68Trp | missense_variant | 3/24 | ENST00000361924.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GOLGA4 | ENST00000361924.7 | c.202C>T | p.Arg68Trp | missense_variant | 3/24 | 1 | NM_002078.5 |
Frequencies
GnomAD3 genomes AF: 0.000697 AC: 106AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000591 AC: 148AN: 250568Hom.: 1 AF XY: 0.000671 AC XY: 91AN XY: 135644
GnomAD4 exome AF: 0.00115 AC: 1686AN: 1461726Hom.: 4 Cov.: 31 AF XY: 0.00116 AC XY: 840AN XY: 727168
GnomAD4 genome AF: 0.000696 AC: 106AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.000618 AC XY: 46AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.268C>T (p.R90W) alteration is located in exon 4 (coding exon 4) of the GOLGA4 gene. This alteration results from a C to T substitution at nucleotide position 268, causing the arginine (R) at amino acid position 90 to be replaced by a tryptophan (W). 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