rs7395206

Variant names:

• chr11-568211-G-A
• rs7395206
• ENST00000500447.3:n.98+141C>T

Your query was ambiguous. Multiple possible variants found:

• chr11-568211-G-A
• chr11-568211-G-C
• chr11-568211-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000500447.3(MIR210HG):​n.98+141C>T variant causes a intron 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 ENST00000500447.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 11 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500447.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR210HG	NR_038262.1		n.106+141C>T		intron	N/A
	MIR210	NR_029623.1		n.-13C>T		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR210HG	ENST00000500447.3	TSL:2	n.98+141C>T		intron	N/A
	MIR210HG	ENST00000528245.3	TSL:3	n.87+141C>T		intron	N/A
	MIR210HG	ENST00000533920.1	TSL:2	n.106+141C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73692 AN: 151244 Hom.: 19918 Cov.: 31

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

GnomAD2 exomes AF: 0.553 AC: 2356 AN: 4258 AF XY: 0.569

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 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

African (AFR) AF: 0.238 AC: 182 AN: 764

American (AMR) AF: 0.404 AC: 528 AN: 1308

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 956 AN: 1470

East Asian (EAS) AF: 0.598 AC: 147 AN: 246

South Asian (SAS) AF: 0.577 AC: 13454 AN: 23336

European-Finnish (FIN) AF: 0.634 AC: 2858 AN: 4508

Middle Eastern (MID) AF: 0.545 AC: 121 AN: 222

European-Non Finnish (NFE) AF: 0.572 AC: 20400 AN: 35652

Other (OTH) AF: 0.556 AC: 1509 AN: 2712

GnomAD4 genome AF: 0.487 AC: 73680 AN: 151360 Hom.: 19910 Cov.: 31 AF XY: 0.493 AC XY: 36426 AN XY: 73940

African (AFR) AF: 0.235 AC: 9742 AN: 41418

American (AMR) AF: 0.454 AC: 6943 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2291 AN: 3458

East Asian (EAS) AF: 0.680 AC: 3439 AN: 5060

South Asian (SAS) AF: 0.602 AC: 2885 AN: 4796

European-Finnish (FIN) AF: 0.670 AC: 6980 AN: 10414

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39617 AN: 67636

Other (OTH) AF: 0.514 AC: 1080 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.1
DANN	Benign	0.93
PhyloP100		0.27
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

Other links and lift over

dbSNP: rs7395206; hg19: chr11-568211;