Variant chr2-38058462-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.812

Variant links:

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 links:

RMDN2-AS1 (HGNC:41150): (RMDN2 antisense RNA 1)

RMDN2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect
RMDN2	NM_001322212.2 linkuse as main transcript	c.1180-8520T>C	intron_variant
RMDN2	NM_144713.5 linkuse as main transcript	c.1714-8520T>C	intron_variant
RMDN2	XM_011532615.4 linkuse as main transcript	c.*28-8520T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
RMDN2	ENST00000234195.7 linkuse as main transcript	c.1714-8520T>C	intron_variant	2
RMDN2	ENST00000469469.1 linkuse as main transcript	n.295-8520T>C	intron_variant, non_coding_transcript_variant	3
RMDN2-AS1	ENST00000601029.1 linkuse as main transcript	n.149+8431A>G	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.765

AC:

116325

AN:

152012

Hom.:

45963

Cov.:

show subpopulations

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.:

AF XY:

0.759

AC XY:

56434

AN XY:

74366

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over