rs1534780

Variant names:

• chr15-93081984-C-G
• rs1534780
• NM_020211.3:c.14+6935G>C

Your query was ambiguous. Multiple possible variants found:

• chr15-93081984-C-G
• chr15-93081984-C-T

Variant summary

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

The NM_020211.3(RGMA):​c.14+6935G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,152 control chromosomes in the GnomAD database, including 11,539 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 0.38 (11539 hom., cov: 34)
• Consequence: RGMA NM_020211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.422 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.14+6935G>C		intron	N/A	NP_064596.2	Q96B86-1
	RGMA	NM_001166287.2		c.-35+6297G>C		intron	N/A	NP_001159759.1	Q96B86-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RGMA	ENST00000329082.12	TSL:1 MANE Select	c.14+6935G>C		intron	N/A	ENSP00000330005.7	Q96B86-1
	RGMA	ENST00000543599.5	TSL:5	c.-35+6297G>C		intron	N/A	ENSP00000442498.1	Q96B86-3
	RGMA	ENST00000555598.1	TSL:4	c.-35+6297G>C		intron	N/A	ENSP00000451709.1	G3V4C2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58273 AN: 152034 Hom.: 11538 Cov.: 34

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.383 AC: 58282 AN: 152152 Hom.: 11539 Cov.: 34 AF XY: 0.382 AC XY: 28446 AN XY: 74384

African (AFR) AF: 0.290 AC: 12049 AN: 41508

American (AMR) AF: 0.417 AC: 6374 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1667 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1862 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4631 AN: 10578

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 29001 AN: 67998

Other (OTH) AF: 0.386 AC: 817 AN: 2116

Alfa AF: 0.406 Hom.: 1556

Bravo AF: 0.381

Asia WGS AF: 0.343 AC: 1193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.66
PhyloP100		-0.40
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: rs1534780; hg19: chr15-93625213;