15-93044800-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596
• Publications: 0 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: 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).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	NM_020211.3	MANE Select	c.*198A>C		3_prime_UTR	Exon 4 of 4	NP_064596.2	Q96B86-1
	RGMA	NM_001166283.2		c.*198A>C		3_prime_UTR	Exon 4 of 4	NP_001159755.1	A0A0A0MTQ4
	RGMA	NM_001166286.2		c.*198A>C		3_prime_UTR	Exon 3 of 3	NP_001159758.1	Q96B86-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	ENST00000329082.12	TSL:1 MANE Select	c.*198A>C		3_prime_UTR	Exon 4 of 4	ENSP00000330005.7	Q96B86-1
	RGMA	ENST00000542321.6	TSL:1	c.*198A>C		3_prime_UTR	Exon 3 of 3	ENSP00000440025.2	Q96B86-3
	RGMA	ENST00000425933.6	TSL:5	c.*198A>C		3_prime_UTR	Exon 4 of 4	ENSP00000404442.2	Q96B86-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000447 AC: 2 AN: 447052 Hom.: 0 Cov.: 4 AF XY: 0.00000851 AC XY: 2 AN XY: 234948

African (AFR) AF: 0.00 AC: 0 AN: 12332

American (AMR) AF: 0.0000544 AC: 1 AN: 18384

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13622

East Asian (EAS) AF: 0.00 AC: 0 AN: 30906

South Asian (SAS) AF: 0.00 AC: 0 AN: 44940

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 30238

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1944

European-Non Finnish (NFE) AF: 0.00000372 AC: 1 AN: 268854

Other (OTH) AF: 0.00 AC: 0 AN: 25832

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
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

Other links and lift over

dbSNP: rs1969589; hg19: chr15-93588030;