rs163077

chr2-38058462-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMDN2	NM_001322212.2	c.1180-8520T>C		intron_variant
RMDN2	NM_144713.5	c.1714-8520T>C		intron_variant
RMDN2	XM_011532615.4	c.*28-8520T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMDN2	ENST00000234195.7	c.1714-8520T>C		intron_variant		2
RMDN2	ENST00000469469.1	n.295-8520T>C		intron_variant, non_coding_transcript_variant		3
RMDN2-AS1	ENST00000601029.1	n.149+8431A>G		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.933

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.762

Alfa AF: 0.751 Hom.: 27999

Bravo AF: 0.771

Asia WGS AF: 0.522 AC: 1819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.44
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163077; hg19: chr2-38285605;