19-9854407-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_058164.4(OLFM2):c.1144G>A(p.Val382Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000192 in 1,614,194 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_058164.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OLFM2 | NM_058164.4 | c.1144G>A | p.Val382Met | missense_variant | Exon 6 of 6 | ENST00000264833.9 | NP_477512.1 | |
OLFM2 | NM_001304347.2 | c.1216G>A | p.Val406Met | missense_variant | Exon 6 of 6 | NP_001291276.1 | ||
OLFM2 | NM_001304348.2 | c.910G>A | p.Val304Met | missense_variant | Exon 5 of 5 | NP_001291277.1 | ||
OLFM2 | XM_047439713.1 | c.940G>A | p.Val314Met | missense_variant | Exon 6 of 6 | XP_047295669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OLFM2 | ENST00000264833.9 | c.1144G>A | p.Val382Met | missense_variant | Exon 6 of 6 | 1 | NM_058164.4 | ENSP00000264833.3 | ||
OLFM2 | ENST00000593091.2 | c.1216G>A | p.Val406Met | missense_variant | Exon 6 of 6 | 5 | ENSP00000465809.2 | |||
OLFM2 | ENST00000590841.5 | c.910G>A | p.Val304Met | missense_variant | Exon 5 of 5 | 2 | ENSP00000464877.1 | |||
OLFM2 | ENST00000592448.1 | n.*549G>A | downstream_gene_variant | 3 | ENSP00000466018.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251462Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461882Hom.: 0 Cov.: 34 AF XY: 0.0000193 AC XY: 14AN XY: 727242
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1144G>A (p.V382M) alteration is located in exon 6 (coding exon 6) of the OLFM2 gene. This alteration results from a G to A substitution at nucleotide position 1144, causing the valine (V) at amino acid position 382 to be replaced by a methionine (M). 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