NM_020211.3:c.*198A>G

Variant names:

• chr15-93044800-T-C
• rs1969589
• NM_020211.3:c.*198A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 7 publications found

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]

ENSG00000257060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020211.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	NM_020211.3	MANE Select	c.*198A>G		3_prime_UTR	Exon 4 of 4	NP_064596.2
	RGMA	NM_001166283.2		c.*198A>G		3_prime_UTR	Exon 4 of 4	NP_001159755.1
	RGMA	NM_001166286.2		c.*198A>G		3_prime_UTR	Exon 3 of 3	NP_001159758.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	ENST00000329082.12	TSL:1 MANE Select	c.*198A>G		3_prime_UTR	Exon 4 of 4	ENSP00000330005.7
	RGMA	ENST00000542321.6	TSL:1	c.*198A>G		3_prime_UTR	Exon 3 of 3	ENSP00000440025.2
	RGMA	ENST00000554387.5	TSL:2	n.*1472A>G		non_coding_transcript_exon	Exon 5 of 5	ENSP00000451505.1

Frequencies

GnomAD3 genomes AF: 0.917 AC: 139542 AN: 152092 Hom.: 65272 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.767

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.936

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.913

GnomAD4 exome AF: 0.896 AC: 400322 AN: 446966 Hom.: 185460 Cov.: 4 AF XY: 0.892 AC XY: 209567 AN XY: 234902

African (AFR) AF: 0.956 AC: 11792 AN: 12332

American (AMR) AF: 0.703 AC: 12927 AN: 18378

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 13076 AN: 13622

East Asian (EAS) AF: 0.356 AC: 11010 AN: 30892

South Asian (SAS) AF: 0.814 AC: 36551 AN: 44916

European-Finnish (FIN) AF: 0.938 AC: 28368 AN: 30234

Middle Eastern (MID) AF: 0.954 AC: 1854 AN: 1944

European-Non Finnish (NFE) AF: 0.972 AC: 261205 AN: 268820

Other (OTH) AF: 0.911 AC: 23539 AN: 25828

GnomAD4 genome AF: 0.917 AC: 139632 AN: 152210 Hom.: 65316 Cov.: 32 AF XY: 0.906 AC XY: 67457 AN XY: 74426

African (AFR) AF: 0.957 AC: 39757 AN: 41546

American (AMR) AF: 0.766 AC: 11700 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3336 AN: 3472

East Asian (EAS) AF: 0.372 AC: 1918 AN: 5152

South Asian (SAS) AF: 0.790 AC: 3807 AN: 4822

European-Finnish (FIN) AF: 0.936 AC: 9940 AN: 10616

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.972 AC: 66132 AN: 68006

Other (OTH) AF: 0.906 AC: 1915 AN: 2114

Alfa AF: 0.904 Hom.: 19815

Bravo AF: 0.905

Asia WGS AF: 0.638 AC: 2223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	16
DANN	Benign	0.79
PhyloP100		0.60
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1969589; hg19: chr15-93588030; COSMIC: COSV61233816; COSMIC: COSV61233816;