2-38050689-T-G

Variant names:

• chr2-38050689-T-G
• rs6741148
• NM_144713.5:c.1714-16293T>G

Variant summary

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

The NM_144713.5(RMDN2):​c.1714-16293T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,090 control chromosomes in the GnomAD database, including 7,775 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 0.22 (7775 hom., cov: 32)
• Consequence: RMDN2 NM_144713.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 15 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RMDN2	NM_144713.5	c.1714-16293T>G		intron_variant	Intron 10 of 10		NP_653314.3
RMDN2	NM_001322212.2	c.1180-16293T>G		intron_variant	Intron 10 of 10		NP_001309141.1
RMDN2	XM_011532614.4	c.1714-4051T>G		intron_variant	Intron 11 of 11		XP_011530916.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RMDN2	ENST00000234195.7	c.1714-16293T>G		intron_variant	Intron 10 of 10	2		ENSP00000234195.3
RMDN2	ENST00000469469.1	n.295-16293T>G		intron_variant	Intron 3 of 3	3
RMDN2-AS1	ENST00000601029.1	n.150-14045A>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32894 AN: 151972 Hom.: 7750 Cov.: 32

Gnomad AFR AF: 0.591

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0702

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0838

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0538

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.217 AC: 32973 AN: 152090 Hom.: 7775 Cov.: 32 AF XY: 0.216 AC XY: 16032 AN XY: 74358

African (AFR) AF: 0.592 AC: 24510 AN: 41430

American (AMR) AF: 0.127 AC: 1938 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0702 AC: 243 AN: 3460

East Asian (EAS) AF: 0.129 AC: 666 AN: 5156

South Asian (SAS) AF: 0.121 AC: 581 AN: 4818

European-Finnish (FIN) AF: 0.0838 AC: 888 AN: 10600

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0538 AC: 3660 AN: 68008

Other (OTH) AF: 0.183 AC: 387 AN: 2116

Alfa AF: 0.107 Hom.: 8892

Bravo AF: 0.238

Asia WGS AF: 0.161 AC: 559 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	0.28
DANN	Benign	0.75
PhyloP100		-0.37
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: rs6741148; hg19: chr2-38277832;