16-85633962-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014615.5(GSE1):c.56C>T(p.Ala19Val) variant causes a missense change. The variant allele was found at a frequency of 0.000101 in 1,613,102 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A19T) has been classified as Uncertain significance.
Frequency
Consequence
NM_014615.5 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 |
---|---|---|---|---|---|---|---|
GSE1 | NM_014615.5 | c.56C>T | p.Ala19Val | missense_variant | 2/16 | ENST00000253458.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSE1 | ENST00000253458.12 | c.56C>T | p.Ala19Val | missense_variant | 2/16 | 5 | NM_014615.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000156 AC: 39AN: 249246Hom.: 0 AF XY: 0.000215 AC XY: 29AN XY: 134982
GnomAD4 exome AF: 0.0000952 AC: 139AN: 1460786Hom.: 0 Cov.: 32 AF XY: 0.000116 AC XY: 84AN XY: 726718
GnomAD4 genome AF: 0.000158 AC: 24AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.56C>T (p.A19V) alteration is located in exon 2 (coding exon 2) of the GSE1 gene. This alteration results from a C to T substitution at nucleotide position 56, causing the alanine (A) at amino acid position 19 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