rs163076

chr2-38055592-T-Achr2-38055592-T-G

Variant summary

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

The NM_144713.5(RMDN2):c.1714-11390T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,976 control chromosomes in the GnomAD database, including 25,015 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 0.56 (25015 hom., cov: 31)
• Consequence: RMDN2 NM_144713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RMDN2	NM_001322212.2	c.1180-11390T>A		intron_variant
RMDN2	NM_144713.5	c.1714-11390T>A		intron_variant
RMDN2	XM_011532615.4	c.*28-11390T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RMDN2	ENST00000234195.7	c.1714-11390T>A		intron_variant		2
RMDN2	ENST00000469469.1	n.295-11390T>A		intron_variant, non_coding_transcript_variant		3
RMDN2-AS1	ENST00000601029.1	n.149+11301A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85770 AN: 151856 Hom.: 25004 Cov.: 31

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.565 AC: 85822 AN: 151976 Hom.: 25015 Cov.: 31 AF XY: 0.559 AC XY: 41564 AN XY: 74290

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.582

Alfa AF: 0.471 Hom.: 1316

Bravo AF: 0.559

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs163076; hg19: chr2-38282735;