rs1979980

Variant names:

• chr5-98771363-A-C
• rs1979980
• ENST00000308234.11:c.5+690A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-98771363-A-C
• chr5-98771363-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001012761.3(RGMB):​c.5+690A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,034 control chromosomes in the GnomAD database, including 19,109 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 0.49 (19109 hom., cov: 32)
• Consequence: RGMB NM_001012761.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

RGMB (HGNC:26896): (repulsive guidance molecule BMP co-receptor b) RGMB is a glycosylphosphatidylinositol (GPI)-anchored member of the repulsive guidance molecule family (see RGMA, MIM 607362) and contributes to the patterning of the developing nervous system (Samad et al., 2005 [PubMed 15671031]).[supplied by OMIM, Apr 2009]

RGMB-AS1 (HGNC:48666): (RGMB antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RGMB	XM_047417125.1	c.-2289A>C		5_prime_UTR_variant	Exon 1 of 4		XP_047273081.1
RGMB	NM_001012761.3	c.5+690A>C		intron_variant	Intron 2 of 4		NP_001012779.2
RGMB	NM_001366509.1	c.5+690A>C		intron_variant	Intron 2 of 4		NP_001353438.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RGMB	ENST00000308234.11	c.5+690A>C		intron_variant	Intron 2 of 4	1		ENSP00000308219.7
RGMB-AS1	ENST00000501938.6	n.468-179T>G		intron_variant	Intron 1 of 1	1
RGMB	ENST00000434027.2	n.653+690A>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74056 AN: 151916 Hom.: 19102 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.487 AC: 74091 AN: 152034 Hom.: 19109 Cov.: 32 AF XY: 0.494 AC XY: 36748 AN XY: 74326

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.678

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.471

Alfa AF: 0.513 Hom.: 40449

Bravo AF: 0.470

Asia WGS AF: 0.508 AC: 1767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.4
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1979980; hg19: chr5-98107067; COSMIC: COSV57564856; COSMIC: COSV57564856;