chr5-176597515-C-T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_052899.3(GPRIN1):c.2320G>A(p.Glu774Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000941 in 1,476,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 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. E774G) has been classified as Uncertain significance.
Frequency
Consequence
NM_052899.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152188Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000190 AC: 2AN: 105136 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.0000944 AC: 125AN: 1324664Hom.: 0 Cov.: 30 AF XY: 0.0000740 AC XY: 48AN XY: 648330 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152188Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74338 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2320G>A (p.E774K) alteration is located in exon 2 (coding exon 1) of the GPRIN1 gene. This alteration results from a G to A substitution at nucleotide position 2320, causing the glutamic acid (E) at amino acid position 774 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