chr2-38001525-A-G

Position:

• chr2-38001525-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170791.3(RMDN2):​c.1045-2466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 152,090 control chromosomes in the GnomAD database, including 18,958 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 0.46 (18958 hom., cov: 32)
• Consequence: RMDN2 NM_001170791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RMDN2	NM_001170791.3	c.1045-2466A>G		intron_variant		ENST00000354545.8	NP_001164262.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMDN2	ENST00000354545.8	c.1045-2466A>G		intron_variant		1	NM_001170791.3	ENSP00000346549.3

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70293 AN: 151970 Hom.: 18928 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.463 AC: 70383 AN: 152090 Hom.: 18958 Cov.: 32 AF XY: 0.466 AC XY: 34659 AN XY: 74346

Gnomad4 AFR AF: 0.719

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.449

Alfa AF: 0.375 Hom.: 2883

Bravo AF: 0.495

Asia WGS AF: 0.583 AC: 2025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.83

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

LitVar

Other links and lift over

dbSNP: rs1374196; hg19: chr2-38228668;