chr17-4558431-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001288702.2(GGT6):c.1084G>A(p.Val362Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,606,262 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001288702.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GGT6 | NM_001288702.2 | c.1084G>A | p.Val362Met | missense_variant | 4/4 | ENST00000381550.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GGT6 | ENST00000381550.8 | c.1084G>A | p.Val362Met | missense_variant | 4/4 | 2 | NM_001288702.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000755 AC: 115AN: 152256Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000706 AC: 172AN: 243652Hom.: 0 AF XY: 0.000754 AC XY: 100AN XY: 132658
GnomAD4 exome AF: 0.00104 AC: 1515AN: 1453888Hom.: 0 Cov.: 30 AF XY: 0.00102 AC XY: 741AN XY: 723576
GnomAD4 genome AF: 0.000755 AC: 115AN: 152374Hom.: 0 Cov.: 33 AF XY: 0.000765 AC XY: 57AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1066G>A (p.V356M) alteration is located in exon 4 (coding exon 4) of the GGT6 gene. This alteration results from a G to A substitution at nucleotide position 1066, causing the valine (V) at amino acid position 356 to be replaced by a methionine (M). 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