Variant 2-55988917-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_126406.1(MIR217HG):n.208+24692C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 481,352 control chromosomes in the GnomAD database, including 199,721 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 0.92 ( 64440 hom., cov: 32)

Exomes 𝑓: 0.91 ( 135281 hom. )

Consequence

MIR217HG
NR_126406.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.205

Variant links:

Genes affected

MIR217HG (HGNC:50537): (MIR217 host gene)

MIR217HG links:

(HGNC:):

links:

MIR216A (HGNC:31593): (microRNA 216a) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR216A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
MIR217HG	NR_126406.1 linkuse as main transcript	n.208+24692C>T	intron_variant, non_coding_transcript_variant
LOC105374690	XR_940109.3 linkuse as main transcript	n.587+36678G>A	intron_variant, non_coding_transcript_variant
MIR216A	NR_029629.1 linkuse as main transcript		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
MIR217HG	ENST00000446139.1 linkuse as main transcript	n.208+24692C>T	intron_variant, non_coding_transcript_variant	5
	ENST00000606639.1 linkuse as main transcript	n.82+36678G>A	intron_variant, non_coding_transcript_variant	1
MIR217HG	ENST00000701602.1 linkuse as main transcript	n.407+4956C>T	intron_variant, non_coding_transcript_variant
MIR216A	ENST00000385063.1 linkuse as main transcript		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.919

AC:

139890

AN:

152148

Hom.:

64384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.957

Gnomad AMI

AF:

0.927

Gnomad AMR

AF:

0.908

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.879

Gnomad SAS

AF:

0.909

Gnomad FIN

AF:

0.885

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.911

Gnomad OTH

AF:

0.900

GnomAD3 exomes

AF:

0.907

AC:

220509

AN:

243126

Hom.:

100075

AF XY:

0.905

AC XY:

119051

AN XY:

131536

show subpopulations

Gnomad AFR exome

AF:

0.958

Gnomad AMR exome

AF:

0.914

Gnomad ASJ exome

AF:

0.881

Gnomad EAS exome

AF:

0.872

Gnomad SAS exome

AF:

0.906

Gnomad FIN exome

AF:

0.879

Gnomad NFE exome

AF:

0.911

Gnomad OTH exome

AF:

0.909

GnomAD4 exome

AF:

0.906

AC:

298269

AN:

329088

Hom.:

135281

Cov.:

AF XY:

0.905

AC XY:

166336

AN XY:

183700

show subpopulations

Gnomad4 AFR exome

AF:

0.955

Gnomad4 AMR exome

AF:

0.913

Gnomad4 ASJ exome

AF:

0.882

Gnomad4 EAS exome

AF:

0.869

Gnomad4 SAS exome

AF:

0.907

Gnomad4 FIN exome

AF:

0.879

Gnomad4 NFE exome

AF:

0.912

Gnomad4 OTH exome

AF:

0.905

GnomAD4 genome

AF:

0.919

AC:

140002

AN:

152264

Hom.:

64440

Cov.:

AF XY:

0.917

AC XY:

68232

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.957

Gnomad4 AMR

AF:

0.909

Gnomad4 ASJ

AF:

0.877

Gnomad4 EAS

AF:

0.879

Gnomad4 SAS

AF:

0.909

Gnomad4 FIN

AF:

0.885

Gnomad4 NFE

AF:

0.911

Gnomad4 OTH

AF:

0.896

Alfa

AF:

0.910

Hom.:

11969

Bravo

AF:

0.922

Asia WGS

AF:

0.906

AC:

3150

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.71

DANN

Benign

0.65

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