Variant rs1979980 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000308234.11(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
ENST00000308234.11 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Variant links:

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 links:

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

RGMB-AS1 links:

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ACMG classification

Classification made for transcript

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/exons	MANE	UniProt
RGMB-AS1	NR_033932.1 linkuse as main transcript	n.464-179T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RGMB-AS1	ENST00000498871.3 linkuse as main transcript	n.351-179T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

74056

AN:

151916

Hom.:

19102

Cov.:

show subpopulations

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.:

AF XY:

0.494

AC XY:

36748

AN XY:

74326

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over