20-34852428-A-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_178026.3(GGT7):c.1430T>A(p.Leu477Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178026.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GGT7 | ENST00000336431.10 | c.1430T>A | p.Leu477Gln | missense_variant | Exon 11 of 15 | 1 | NM_178026.3 | ENSP00000338964.5 | ||
GGT7 | ENST00000469018.5 | n.53T>A | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 | ENSP00000486589.1 | ||||
GGT7 | ENST00000470952.2 | c.-157T>A | upstream_gene_variant | 5 | ENSP00000486190.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251266Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135838
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461800Hom.: 0 Cov.: 33 AF XY: 0.0000151 AC XY: 11AN XY: 727206
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1430T>A (p.L477Q) alteration is located in exon 11 (coding exon 11) of the GGT7 gene. This alteration results from a T to A substitution at nucleotide position 1430, causing the leucine (L) at amino acid position 477 to be replaced by a glutamine (Q). 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