rs59393160

Positions:

• chr2-37952271-CTG-C
• chr2-37952271-CTG-CTGTG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001170791.3(RMDN2):​c.453-21767_453-21766del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 1,402,382 control chromosomes in the GnomAD database, including 155,148 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.40 (12721 hom., cov: 0)
  • Exomes 𝑓: 0.47 (142427 hom.)
• Consequence: RMDN2 NM_001170791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

RMDN2 (HGNC:26567): (regulator of microtubule dynamics 2) Enables microtubule binding activity. Located in Golgi apparatus; cytosol; and spindle. [provided by Alliance of Genome Resources, Apr 2022]

RMDN2-AS1 (HGNC:41150): (RMDN2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMDN2	NM_001170791.3	c.453-21767_453-21766del		intron_variant		ENST00000354545.8
RMDN2-AS1	NR_102712.1	n.323-1736_323-1735del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMDN2	ENST00000354545.8	c.453-21767_453-21766del		intron_variant		1	NM_001170791.3	P1
RMDN2-AS1	ENST00000630021.2	n.427-1736_427-1735del		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59885 AN: 151540 Hom.: 12718 Cov.: 0

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.426

GnomAD3 exomes AF: 0.423 AC: 91997 AN: 217432 Hom.: 20790 AF XY: 0.435 AC XY: 51828 AN XY: 119144

Gnomad AFR exome AF: 0.271

Gnomad AMR exome AF: 0.405

Gnomad ASJ exome AF: 0.347

Gnomad EAS exome AF: 0.0800

Gnomad SAS exome AF: 0.551

Gnomad FIN exome AF: 0.372

Gnomad NFE exome AF: 0.488

Gnomad OTH exome AF: 0.428

GnomAD4 exome AF: 0.467 AC: 584159 AN: 1250724 Hom.: 142427 AF XY: 0.470 AC XY: 295465 AN XY: 628118

Gnomad4 AFR exome AF: 0.270

Gnomad4 AMR exome AF: 0.404

Gnomad4 ASJ exome AF: 0.330

Gnomad4 EAS exome AF: 0.0959

Gnomad4 SAS exome AF: 0.540

Gnomad4 FIN exome AF: 0.380

Gnomad4 NFE exome AF: 0.494

Gnomad4 OTH exome AF: 0.437

GnomAD4 genome AF: 0.395 AC: 59908 AN: 151658 Hom.: 12721 Cov.: 0 AF XY: 0.390 AC XY: 28877 AN XY: 74104

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0881

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.428

Alfa AF: 0.431 Hom.: 2665

Bravo AF: 0.388

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs59393160; hg19: chr2-38179414;