2-38065619-C-T

Variant names:

• chr2-38065619-C-T
• rs163086
• NM_144713.5:c.1714-1363C>T

Variant summary

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

The NM_144713.5(RMDN2):​c.1714-1363C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,126 control chromosomes in the GnomAD database, including 2,802 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 0.19 (2802 hom., cov: 32)
• Consequence: RMDN2 NM_144713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 3 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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RMDN2	NM_144713.5	c.1714-1363C>T		intron_variant	Intron 10 of 10		NP_653314.3
RMDN2	NM_001322212.2	c.1180-1363C>T		intron_variant	Intron 10 of 10		NP_001309141.1
RMDN2	XM_011532615.4	c.*28-1363C>T		intron_variant	Intron 13 of 13		XP_011530917.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMDN2	ENST00000234195.7	c.1714-1363C>T		intron_variant	Intron 10 of 10	2		ENSP00000234195.3
RMDN2	ENST00000469469.1	n.295-1363C>T		intron_variant	Intron 3 of 3	3
RMDN2-AS1	ENST00000601029.1	n.149+1274G>A		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28462 AN: 152008 Hom.: 2801 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.187 AC: 28484 AN: 152126 Hom.: 2802 Cov.: 32 AF XY: 0.180 AC XY: 13359 AN XY: 74370

African (AFR) AF: 0.203 AC: 8435 AN: 41492

American (AMR) AF: 0.169 AC: 2586 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 797 AN: 3468

East Asian (EAS) AF: 0.0157 AC: 81 AN: 5172

South Asian (SAS) AF: 0.107 AC: 516 AN: 4824

European-Finnish (FIN) AF: 0.124 AC: 1311 AN: 10586

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14207 AN: 67980

Other (OTH) AF: 0.201 AC: 426 AN: 2116

Alfa AF: 0.198 Hom.: 662

Bravo AF: 0.194

Asia WGS AF: 0.0790 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		0.028
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs163086; hg19: chr2-38292762;