15-93070898-C-T

Variant names:

• chr15-93070898-C-T
• rs3887013
• NM_020211.3:c.130+2018G>A

Variant summary

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

The NM_020211.3(RGMA):​c.130+2018G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,184 control chromosomes in the GnomAD database, including 1,995 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 0.14 (1995 hom., cov: 33)
• Consequence: RGMA NM_020211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• Publications: 8 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	NM_020211.3	MANE Select	c.130+2018G>A		intron	N/A	NP_064596.2	Q96B86-1
	RGMA	NM_001166283.2		c.154+2018G>A		intron	N/A	NP_001159755.1	A0A0A0MTQ4
	RGMA	NM_001166286.2		c.82+2018G>A		intron	N/A	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.130+2018G>A		intron	N/A	ENSP00000330005.7	Q96B86-1
	RGMA	ENST00000542321.6	TSL:1	c.82+2018G>A		intron	N/A	ENSP00000440025.2	Q96B86-3
	RGMA	ENST00000556658.1	TSL:1	c.-626+2018G>A		intron	N/A	ENSP00000456290.1	F5H7G2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21785 AN: 152066 Hom.: 1984 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.164

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.143 AC: 21828 AN: 152184 Hom.: 1995 Cov.: 33 AF XY: 0.141 AC XY: 10510 AN XY: 74414

African (AFR) AF: 0.252 AC: 10472 AN: 41480

American (AMR) AF: 0.112 AC: 1719 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 637 AN: 3472

East Asian (EAS) AF: 0.0614 AC: 318 AN: 5182

South Asian (SAS) AF: 0.182 AC: 876 AN: 4822

European-Finnish (FIN) AF: 0.0420 AC: 446 AN: 10612

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6876 AN: 68016

Other (OTH) AF: 0.168 AC: 354 AN: 2110

Alfa AF: 0.114 Hom.: 1954

Bravo AF: 0.152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.066
DANN	Benign	0.76
PhyloP100		-3.2
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: rs3887013; hg19: chr15-93614127;