16-83960987-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_182981.3(OSGIN1):c.403G>A(p.Glu135Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000942 in 1,613,376 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182981.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OSGIN1 | ENST00000393306.6 | c.403G>A | p.Glu135Lys | missense_variant | Exon 5 of 6 | 1 | NM_182981.3 | ENSP00000376983.1 | ||
OSGIN1 | ENST00000361711.7 | c.403G>A | p.Glu135Lys | missense_variant | Exon 5 of 6 | 2 | ENSP00000355374.3 | |||
OSGIN1 | ENST00000565123.5 | c.403G>A | p.Glu135Lys | missense_variant | Exon 5 of 5 | 2 | ENSP00000462048.1 | |||
OSGIN1 | ENST00000343939.6 | n.1035G>A | non_coding_transcript_exon_variant | Exon 6 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152154Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 250638Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135760
GnomAD4 exome AF: 0.0000917 AC: 134AN: 1461104Hom.: 1 Cov.: 31 AF XY: 0.000110 AC XY: 80AN XY: 726858
GnomAD4 genome AF: 0.000118 AC: 18AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.403G>A (p.E135K) alteration is located in exon 5 (coding exon 4) of the OSGIN1 gene. This alteration results from a G to A substitution at nucleotide position 403, causing the glutamic acid (E) at amino acid position 135 to be replaced by a lysine (K). 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