16-85654300-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014615.5(GSE1):c.449G>A(p.Ser150Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000853 in 1,605,424 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. S150I) 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.449G>A | p.Ser150Asn | missense_variant | 4/16 | ENST00000253458.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GSE1 | ENST00000253458.12 | c.449G>A | p.Ser150Asn | missense_variant | 4/16 | 5 | NM_014615.5 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000201 AC: 47AN: 233628Hom.: 0 AF XY: 0.000165 AC XY: 21AN XY: 127528
GnomAD4 exome AF: 0.0000867 AC: 126AN: 1453220Hom.: 0 Cov.: 32 AF XY: 0.0000830 AC XY: 60AN XY: 722582
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152204Hom.: 0 Cov.: 31 AF XY: 0.0000807 AC XY: 6AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2021 | The c.449G>A (p.S150N) alteration is located in exon 4 (coding exon 4) of the GSE1 gene. This alteration results from a G to A substitution at nucleotide position 449, causing the serine (S) at amino acid position 150 to be replaced by an asparagine (N). 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