Variant 2-55988955-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_029629.1(MIR216A):n.105T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 511,260 control chromosomes in the GnomAD database, including 1,351 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 0.084 ( 818 hom., cov: 32)

Exomes 𝑓: 0.047 ( 533 hom. )

Consequence

MIR216A
NR_029629.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Variant links:

Genes affected

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:

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

MIR217HG links:

(HGNC:):

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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
MIR216A	NR_029629.1 linkuse as main transcript	n.105T>A	non_coding_transcript_exon_variant	1/1
MIR217HG	NR_126406.1 linkuse as main transcript	n.208+24654T>A	intron_variant, non_coding_transcript_variant
LOC105374690	XR_940109.3 linkuse as main transcript	n.587+36716A>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
MIR216A	ENST00000385063.1 linkuse as main transcript	n.105T>A	non_coding_transcript_exon_variant	1/1
MIR217HG	ENST00000446139.1 linkuse as main transcript	n.208+24654T>A	intron_variant, non_coding_transcript_variant		5
	ENST00000606639.1 linkuse as main transcript	n.82+36716A>T	intron_variant, non_coding_transcript_variant		1
MIR217HG	ENST00000701602.1 linkuse as main transcript	n.407+4918T>A	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0844

AC:

12847

AN:

152126

Hom.:

818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.0756

Gnomad ASJ

AF:

0.0597

Gnomad EAS

AF:

0.00173

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0246

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0491

Gnomad OTH

AF:

0.0789

GnomAD3 exomes

AF:

0.0503

AC:

12450

AN:

247660

Hom.:

509

AF XY:

0.0486

AC XY:

6501

AN XY:

133902

show subpopulations

Gnomad AFR exome

AF:

0.184

Gnomad AMR exome

AF:

0.0433

Gnomad ASJ exome

AF:

0.0628

Gnomad EAS exome

AF:

0.000601

Gnomad SAS exome

AF:

0.0431

Gnomad FIN exome

AF:

0.0242

Gnomad NFE exome

AF:

0.0470

Gnomad OTH exome

AF:

0.0512

GnomAD4 exome

AF:

0.0465

AC:

16697

AN:

359016

Hom.:

533

Cov.:

AF XY:

0.0460

AC XY:

9257

AN XY:

201180

show subpopulations

Gnomad4 AFR exome

AF:

0.178

Gnomad4 AMR exome

AF:

0.0438

Gnomad4 ASJ exome

AF:

0.0608

Gnomad4 EAS exome

AF:

0.000636

Gnomad4 SAS exome

AF:

0.0429

Gnomad4 FIN exome

AF:

0.0249

Gnomad4 NFE exome

AF:

0.0466

Gnomad4 OTH exome

AF:

0.0529

GnomAD4 genome

AF:

0.0845

AC:

12863

AN:

152244

Hom.:

818

Cov.:

AF XY:

0.0817

AC XY:

6083

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.180

Gnomad4 AMR

AF:

0.0757

Gnomad4 ASJ

AF:

0.0597

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.0439

Gnomad4 FIN

AF:

0.0246

Gnomad4 NFE

AF:

0.0491

Gnomad4 OTH

AF:

0.0781

Alfa

AF:

0.0421

Hom.:

Bravo

AF:

0.0909

Asia WGS

AF:

0.0310

AC:

106

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

DANN

Benign

0.87

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