rs1969589
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020211.3(RGMA):c.*198A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 599,176 control chromosomes in the GnomAD database, including 250,776 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.92 ( 65316 hom., cov: 32)
Exomes 𝑓: 0.90 ( 185460 hom. )
Consequence
RGMA
NM_020211.3 3_prime_UTR
NM_020211.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.596
Genes affected
RGMA (HGNC:30308): (repulsive guidance molecule BMP co-receptor a) This gene encodes a member of the repulsive guidance molecule family. The encoded protein is a glycosylphosphatidylinositol-anchored glycoprotein that functions as an axon guidance protein in the developing and adult central nervous system. This protein may also function as a tumor suppressor in some cancers. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGMA | NM_020211.3 | c.*198A>G | 3_prime_UTR_variant | 4/4 | ENST00000329082.12 | NP_064596.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGMA | ENST00000329082 | c.*198A>G | 3_prime_UTR_variant | 4/4 | 1 | NM_020211.3 | ENSP00000330005.7 |
Frequencies
GnomAD3 genomes AF: 0.917 AC: 139542AN: 152092Hom.: 65272 Cov.: 32
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GnomAD4 exome AF: 0.896 AC: 400322AN: 446966Hom.: 185460 Cov.: 4 AF XY: 0.892 AC XY: 209567AN XY: 234902
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GnomAD4 genome AF: 0.917 AC: 139632AN: 152210Hom.: 65316 Cov.: 32 AF XY: 0.906 AC XY: 67457AN XY: 74426
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at