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rs7395206

chr11-568211-G-Achr11-568211-G-Cchr11-568211-G-T

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

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.274
Variant links:
Genes affected
MIR210HG (HGNC:39524): (MIR210 host gene)
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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 UniProt
MIR210HGNR_038262.1 linkuse as main transcriptn.106+141C>T intron_variant, non_coding_transcript_variant
MIR210NR_029623.1 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MIR210HGENST00000665964.2 linkuse as main transcriptn.98+141C>T intron_variant, non_coding_transcript_variant
MIR210ENST00000362168.1 linkuse as main transcript upstream_gene_variant

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.487
AC:
73692
AN:
151244
Hom.:
19918
Cov.:
31
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.:
0
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
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.487
AC:
73680
AN:
151360
Hom.:
19910
Cov.:
31
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.

Other links and lift over

dbSNP: rs7395206; hg19: chr11-568211; API