Genetic Variant RMDN2:c.453-21767_453-21766delGT (chr2-37952271-CTG-C) – ACMG Classification: Benign (-8 pts)

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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.323

Publications

4 publications found

Variant links:

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 links:

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

RMDN2-AS1 links:

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ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
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.:

show subpopulations

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

show subpopulations

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

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

14941

29882

44823

59764

74705

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

12644

25288

37932

50576

63220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.395

AC:

59908

AN:

151658

Hom.:

12721

Cov.:

AF XY:

0.390

AC XY:

28877

AN XY:

74104

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1775

3551

5326

7102

8877

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

578

1156

1734

2312

2890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over