chr14-30615408-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017769.5(G2E3):c.1733C>T(p.Ala578Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,609,182 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_017769.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
G2E3 | NM_017769.5 | c.1733C>T | p.Ala578Val | missense_variant | 14/15 | ENST00000206595.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
G2E3 | ENST00000206595.11 | c.1733C>T | p.Ala578Val | missense_variant | 14/15 | 1 | NM_017769.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000100 AC: 25AN: 249310Hom.: 0 AF XY: 0.0000668 AC XY: 9AN XY: 134792
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1457066Hom.: 0 Cov.: 28 AF XY: 0.0000124 AC XY: 9AN XY: 725022
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.1733C>T (p.A578V) alteration is located in exon 14 (coding exon 13) of the G2E3 gene. This alteration results from a C to T substitution at nucleotide position 1733, causing the alanine (A) at amino acid position 578 to be replaced by a valine (V). 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