9-114329909-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_000608.4(ORM2):c.5C>T(p.Ala2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A2A) has been classified as Likely benign.
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: 0.00 AC: 1AN: 110848Hom.: 0 Cov.: 14 FAILED QC
GnomAD3 exomes AF: 0.0000157 AC: 2AN: 127292Hom.: 0 AF XY: 0.0000300 AC XY: 2AN XY: 66596
GnomAD4 exome AF: 0.00000552 AC: 7AN: 1268336Hom.: 0 Cov.: 20 AF XY: 0.00000482 AC XY: 3AN XY: 622492
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000902 AC: 1AN: 110848Hom.: 0 Cov.: 14 AF XY: 0.00 AC XY: 0AN XY: 51862
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.5C>T (p.A2V) alteration is located in exon 1 (coding exon 1) of the ORM2 gene. This alteration results from a C to T substitution at nucleotide position 5, causing the alanine (A) at amino acid position 2 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