Genetic Variant MIR9-2HG:n.217+54922G>C (chr5-88616114-C-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000502301.6(MIR9-2HG):n.217+54922G>C variant causes a intron change. 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 0.0 ( 0 hom., cov: 17)

Failed GnomAD Quality Control

Consequence

MIR9-2HG
ENST00000502301.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Publications

1 publications found

Variant links:

Genes affected

MIR9-2HG (HGNC:42810): (MIR9-2 host gene) This is an evolutionarily conserved gene that produces alternatively spliced long non-coding RNAs that may be expressed predominantly in the brain and visual cortex. These transcripts may be involved in tumorigenesis, as depletion by siRNA suppressed glioma cell division. Transcripts may also bind to and regulate the activity of miR-411-5p and argonaut 2, thereby altering the expression of genes involved in tumor growth. [provided by RefSeq, Nov 2017]

MIR9-2HG links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR9-2HG	NR_015436.2 link	n.282+54922G>C	intron_variant	Intron 3 of 4
MIR9-2HG	NR_152235.1 link	n.218+54922G>C	intron_variant	Intron 2 of 3
MIR9-2HG	NR_152238.1 link	n.215+54922G>C	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
MIR9-2HG	ENST00000502301.6 link	n.217+54922G>C	intron_variant	Intron 3 of 4	4
MIR9-2HG	ENST00000506014.6 link	n.151+54922G>C	intron_variant	Intron 2 of 3	4
MIR9-2HG	ENST00000506664.8 link	n.107+62234G>C	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

75982

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

75982

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

36768

African (AFR)

AF:

0.00

AC:

AN:

29116

American (AMR)

AF:

0.00

AC:

AN:

5522

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2010

East Asian (EAS)

AF:

0.00

AC:

AN:

2780

South Asian (SAS)

AF:

0.00

AC:

AN:

2782

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

200

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

28604

Other (OTH)

AF:

0.00

AC:

AN:

1026

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

5.3

(source)

DANN

Benign

0.81

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over