rs6873523

Variant names:

• chr5-178145926-C-A
• rs6873523
• NM_022762.5:c.695-188C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-178145926-C-A
• chr5-178145926-C-G
• chr5-178145926-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000313386.9(RMND5B):​c.695-188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RMND5B ENST00000313386.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235
• Publications: 3 publications found

Genes affected

RMND5B (HGNC:26181): (required for meiotic nuclear division 5 homolog B) Predicted to enable metal ion binding activity and ubiquitin protein ligase activity. Predicted to contribute to ubiquitin-protein transferase activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000313386.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMND5B	NM_022762.5	MANE Select	c.695-188C>A		intron	N/A	NP_073599.2
	RMND5B	NM_001288794.2		c.695-188C>A		intron	N/A	NP_001275723.1
	RMND5B	NM_001288795.2		c.656-188C>A		intron	N/A	NP_001275724.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMND5B	ENST00000313386.9	TSL:1 MANE Select	c.695-188C>A		intron	N/A	ENSP00000320623.4
	RMND5B	ENST00000515098.5	TSL:2	c.695-188C>A		intron	N/A	ENSP00000420875.1
	RMND5B	ENST00000542098.2	TSL:5	c.656-188C>A		intron	N/A	ENSP00000437630.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 420316 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 218252

African (AFR) AF: 0.00 AC: 0 AN: 12256

American (AMR) AF: 0.00 AC: 0 AN: 18000

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12824

East Asian (EAS) AF: 0.00 AC: 0 AN: 30554

South Asian (SAS) AF: 0.00 AC: 0 AN: 36360

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 28236

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1814

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 255644

Other (OTH) AF: 0.00 AC: 0 AN: 24628

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.78
PhyloP100		-0.23
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs6873523; hg19: chr5-177572927;