2-37981090-T-C

Variant names:

• chr2-37981090-T-C
• rs1446297
• NM_001170791.3:c.731-193T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170791.3(RMDN2):​c.731-193T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,060 control chromosomes in the GnomAD database, including 15,145 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 0.42 (15145 hom., cov: 32)
• Consequence: RMDN2 NM_001170791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275
• Publications: 7 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.76 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.731-193T>C		intron	N/A	NP_001164262.1
	RMDN2	NM_144713.5		c.1265-193T>C		intron	N/A	NP_653314.3
	RMDN2	NM_001170792.3		c.731-193T>C		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.731-193T>C		intron	N/A	ENSP00000346549.3
	RMDN2	ENST00000406384.5	TSL:1	c.731-193T>C		intron	N/A	ENSP00000386004.1
	RMDN2	ENST00000417700.6	TSL:1	c.296-193T>C		intron	N/A	ENSP00000392977.2

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64361 AN: 151942 Hom.: 15141 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.424 AC: 64416 AN: 152060 Hom.: 15145 Cov.: 32 AF XY: 0.430 AC XY: 31930 AN XY: 74330

African (AFR) AF: 0.581 AC: 24082 AN: 41460

American (AMR) AF: 0.492 AC: 7521 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1666 AN: 3464

East Asian (EAS) AF: 0.780 AC: 4041 AN: 5180

South Asian (SAS) AF: 0.374 AC: 1803 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3558 AN: 10562

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20502 AN: 67972

Other (OTH) AF: 0.416 AC: 880 AN: 2116

Alfa AF: 0.352 Hom.: 31926

Bravo AF: 0.449

Asia WGS AF: 0.573 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.77
PhyloP100		-0.28
Mutation Taster		=100/0	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: rs1446297; hg19: chr2-38208233;