rs59393160

Variant names:

• chr2-37952271-CTG-C
• rs59393160
• NM_001170791.3:c.453-21767_453-21766delGT

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001170791.3(RMDN2):​c.453-21767_453-21766delGT 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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001170791.3. 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
	RMDN2	NM_001170791.3	MANE Select	c.453-21767_453-21766delGT		intron	N/A	NP_001164262.1
	RMDN2	NM_144713.5		c.986+72_986+73delGT		intron	N/A	NP_653314.3
	RMDN2	NM_001170792.3		c.453-21767_453-21766delGT		intron	N/A	NP_001164263.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMDN2	ENST00000354545.8	TSL:1 MANE Select	c.453-21767_453-21766delGT		intron	N/A	ENSP00000346549.3
	RMDN2	ENST00000406384.5	TSL:1	c.453-21767_453-21766delGT		intron	N/A	ENSP00000386004.1
	RMDN2	ENST00000417700.6	TSL:1	c.17+1678_17+1679delGT		intron	N/A	ENSP00000392977.2

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

GnomAD2 exomes AF: 0.423 AC: 91997 AN: 217432 AF XY: 0.435

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 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

African (AFR) AF: 0.270 AC: 7628 AN: 28302

American (AMR) AF: 0.404 AC: 14873 AN: 36858

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 7477 AN: 22638

East Asian (EAS) AF: 0.0959 AC: 3689 AN: 38480

South Asian (SAS) AF: 0.540 AC: 41930 AN: 77580

European-Finnish (FIN) AF: 0.380 AC: 19393 AN: 50986

Middle Eastern (MID) AF: 0.446 AC: 2325 AN: 5216

European-Non Finnish (NFE) AF: 0.494 AC: 463826 AN: 937974

Other (OTH) AF: 0.437 AC: 23018 AN: 52690

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

African (AFR) AF: 0.274 AC: 11357 AN: 41396

American (AMR) AF: 0.411 AC: 6254 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3468

East Asian (EAS) AF: 0.0881 AC: 455 AN: 5166

South Asian (SAS) AF: 0.522 AC: 2514 AN: 4814

European-Finnish (FIN) AF: 0.365 AC: 3837 AN: 10522

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 32987 AN: 67770

Other (OTH) AF: 0.428 AC: 899 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.32
Mutation Taster		=193/7	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: rs59393160; hg19: chr2-38179414;