rs163077

Variant names:

• chr2-38058462-T-C
• rs163077
• NM_144713.5:c.1714-8520T>C

Variant summary

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

The NM_144713.5(RMDN2):​c.1714-8520T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,130 control chromosomes in the GnomAD database, including 46,015 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 0.77 (46015 hom., cov: 32)
• Consequence: RMDN2 NM_144713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812
• Publications: 13 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144713.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMDN2	NM_144713.5		c.1714-8520T>C		intron	N/A	NP_653314.3
	RMDN2	NM_001322212.2		c.1180-8520T>C		intron	N/A	NP_001309141.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RMDN2	ENST00000234195.7	TSL:2	c.1714-8520T>C		intron	N/A	ENSP00000234195.3
	RMDN2	ENST00000469469.1	TSL:3	n.295-8520T>C		intron	N/A
	RMDN2-AS1	ENST00000601029.1	TSL:5	n.149+8431A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116325 AN: 152012 Hom.: 45963 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.828

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.765 AC: 116434 AN: 152130 Hom.: 46015 Cov.: 32 AF XY: 0.759 AC XY: 56434 AN XY: 74366

African (AFR) AF: 0.933 AC: 38782 AN: 41548

American (AMR) AF: 0.697 AC: 10652 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2794 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1286 AN: 5162

South Asian (SAS) AF: 0.739 AC: 3563 AN: 4820

European-Finnish (FIN) AF: 0.675 AC: 7119 AN: 10554

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.732 AC: 49785 AN: 67982

Other (OTH) AF: 0.762 AC: 1600 AN: 2100

Alfa AF: 0.744 Hom.: 95208

Bravo AF: 0.771

Asia WGS AF: 0.522 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.44
DANN	Benign	0.29
PhyloP100		-0.81
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: rs163077; hg19: chr2-38285605;