Variant chr11-568211-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_038262.1(MIR210HG):n.106+141C>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 0.514 in 221,578 control chromosomes in the GnomAD database, including 31,782 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 0.49 ( 19910 hom., cov: 31)

Exomes 𝑓: 0.57 ( 11872 hom. )

Consequence

MIR210HG
NR_038262.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274

Variant links:

Genes affected

MIR210HG (HGNC:39524): (MIR210 host gene)

MIR210HG links:

MIR210 (HGNC:31587): (microRNA 210) 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]

MIR210 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR210HG	NR_038262.1 linkuse as main transcript	n.106+141C>T		intron_variant, non_coding_transcript_variant
MIR210	NR_029623.1 linkuse as main transcript			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR210HG	ENST00000665964.2 linkuse as main transcript	n.98+141C>T		intron_variant, non_coding_transcript_variant
MIR210	ENST00000362168.1 linkuse as main transcript			upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

73692

AN:

151244

Hom.:

19918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.236

Gnomad AMI

AF:

0.610

Gnomad AMR

AF:

0.455

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.680

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.586

Gnomad OTH

AF:

0.515

GnomAD3 exomes

AF:

0.553

AC:

2356

AN:

4258

Hom.:

685

AF XY:

0.569

AC XY:

1311

AN XY:

2306

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.415

Gnomad ASJ exome

AF:

0.710

Gnomad EAS exome

AF:

0.614

Gnomad SAS exome

AF:

0.561

Gnomad FIN exome

AF:

0.673

Gnomad NFE exome

AF:

0.610

Gnomad OTH exome

AF:

0.690

GnomAD4 exome

AF:

0.572

AC:

40155

AN:

70218

Hom.:

11872

Cov.:

AF XY:

0.575

AC XY:

24467

AN XY:

42562

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.404

Gnomad4 ASJ exome

AF:

0.650

Gnomad4 EAS exome

AF:

0.598

Gnomad4 SAS exome

AF:

0.577

Gnomad4 FIN exome

AF:

0.634

Gnomad4 NFE exome

AF:

0.572

Gnomad4 OTH exome

AF:

0.556

GnomAD4 genome

AF:

0.487

AC:

73680

AN:

151360

Hom.:

19910

Cov.:

AF XY:

0.493

AC XY:

36426

AN XY:

73940

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.454

Gnomad4 ASJ

AF:

0.663

Gnomad4 EAS

AF:

0.680

Gnomad4 SAS

AF:

0.602

Gnomad4 FIN

AF:

0.670

Gnomad4 NFE

AF:

0.586

Gnomad4 OTH

AF:

0.514

Alfa

AF:

0.517

Hom.:

2691

Bravo

AF:

0.463

Asia WGS

AF:

0.575

AC:

1997

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

8.1

DANN

Benign

0.93

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.4

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