Genetic Variant RGMA:c.*198A>C (chr15-93044800-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020211.3(RGMA):c.*198A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000447 in 447,052 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000045 ( 0 hom. )

Consequence

RGMA
NM_020211.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.596

Publications

0 publications found

Variant links:

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]

RGMA links:

ENSG00000257060 (HGNC:):

ENSG00000257060 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGMA	NM_020211.3 link	c.*198A>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000329082.12	NP_064596.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGMA	ENST00000329082.12 link	c.*198A>C		3_prime_UTR_variant	Exon 4 of 4	1	NM_020211.3	ENSP00000330005.7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000447

AC:

AN:

447052

Hom.:

Cov.:

AF XY:

0.00000851

AC XY:

AN XY:

234948

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

12332

American (AMR)

AF:

0.0000544

AC:

AN:

18384

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13622

East Asian (EAS)

AF:

0.00

AC:

AN:

30906

South Asian (SAS)

AF:

0.00

AC:

AN:

44940

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30238

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1944

European-Non Finnish (NFE)

AF:

0.00000372

AC:

AN:

268854

Other (OTH)

AF:

0.00

AC:

AN:

25832

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over