chr15-93045144-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020211.3(RGMA):āc.1207A>Cā(p.Met403Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,602,386 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020211.3 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: 0.000210 AC: 32AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 50AN: 228414Hom.: 0 AF XY: 0.000194 AC XY: 24AN XY: 123900
GnomAD4 exome AF: 0.000117 AC: 169AN: 1450338Hom.: 0 Cov.: 35 AF XY: 0.000104 AC XY: 75AN XY: 720344
GnomAD4 genome AF: 0.000210 AC: 32AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2024 | The c.1231A>C (p.M411L) alteration is located in exon 4 (coding exon 4) of the RGMA gene. This alteration results from a A to C substitution at nucleotide position 1231, causing the methionine (M) at amino acid position 411 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