9-114329983-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000608.4(ORM2):c.79G>C(p.Val27Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 1,578,034 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 (★).
Frequency
Consequence
NM_000608.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000223 AC: 3AN: 134446Hom.: 0 Cov.: 20
GnomAD3 exomes AF: 0.0000485 AC: 11AN: 226788Hom.: 0 AF XY: 0.0000324 AC XY: 4AN XY: 123308
GnomAD4 exome AF: 0.00000970 AC: 14AN: 1443588Hom.: 0 Cov.: 28 AF XY: 0.00000976 AC XY: 7AN XY: 716874
GnomAD4 genome AF: 0.0000223 AC: 3AN: 134446Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 64842
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.79G>C (p.V27L) alteration is located in exon 1 (coding exon 1) of the ORM2 gene. This alteration results from a G to C substitution at nucleotide position 79, causing the valine (V) at amino acid position 27 to be replaced by a leucine (L). 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