chr2-37981090-T-C

Position:

• chr2-37981090-T-C

Variant summary

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

The NM_001170791.3(RMDN2):​c.731-193T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 152,060 control chromosomes in the GnomAD database, including 15,145 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 0.42 (15145 hom., cov: 32)
• Consequence: RMDN2 NM_001170791.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.275

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 (EAS) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RMDN2	NM_001170791.3	c.731-193T>C		intron_variant		ENST00000354545.8	NP_001164262.1
RMDN2-AS1	NR_102712.1	n.259-17935A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RMDN2	ENST00000354545.8	c.731-193T>C		intron_variant		1	NM_001170791.3	ENSP00000346549	P1
RMDN2-AS1	ENST00000630021.2	n.325-17897A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64361 AN: 151942 Hom.: 15141 Cov.: 32

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.424 AC: 64416 AN: 152060 Hom.: 15145 Cov.: 32 AF XY: 0.430 AC XY: 31930 AN XY: 74330

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.492

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.416

Alfa AF: 0.335 Hom.: 18364

Bravo AF: 0.449

Asia WGS AF: 0.573 AC: 1992 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	1.8
DANN	Benign	0.77

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: rs1446297; hg19: chr2-38208233;