9-120605605-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001080497.3(MEGF9):āc.1394T>Cā(p.Leu465Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000314 in 1,592,206 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 (ā ).
Frequency
Consequence
NM_001080497.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000477 AC: 1AN: 209538Hom.: 0 AF XY: 0.00000888 AC XY: 1AN XY: 112648
GnomAD4 exome AF: 0.00000278 AC: 4AN: 1439844Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 714110
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2024 | The c.1394T>C (p.L465S) alteration is located in exon 6 (coding exon 6) of the MEGF9 gene. This alteration results from a T to C substitution at nucleotide position 1394, causing the leucine (L) at amino acid position 465 to be replaced by a serine (S). 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