chr15-42330588-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_198141.3(GANC):c.1657G>A(p.Ala553Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198141.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GANC | NM_198141.3 | c.1657G>A | p.Ala553Thr | missense_variant | 15/24 | ENST00000318010.13 | |
GANC | NM_001393928.1 | c.1657G>A | p.Ala553Thr | missense_variant | 16/25 | ||
GANC | NM_001393929.1 | c.1657G>A | p.Ala553Thr | missense_variant | 16/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GANC | ENST00000318010.13 | c.1657G>A | p.Ala553Thr | missense_variant | 15/24 | 1 | NM_198141.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249982Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135142
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460458Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726606
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2021 | The c.1657G>A (p.A553T) alteration is located in exon 15 (coding exon 15) of the GANC gene. This alteration results from a G to A substitution at nucleotide position 1657, causing the alanine (A) at amino acid position 553 to be replaced by a threonine (T). 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