1-209432291-TAGCAGCAGCAGCAGCAGCAGCAGCAGC-TAGCAGCAGCAGCAGCAGCAGCAGCAGCAGC

Variant names:

• chr1-209432291-T-TAGC
• rs3842530
• ENST00000366437.8:n.677_679dupGCA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000366437.8(MIR205HG):​n.677_679dupGCA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.069 (1124 hom., cov: 0)
  • Exomes 𝑓: 0.0093 (455 hom.)
• Consequence: MIR205HG ENST00000366437.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 10 publications found

Genes affected

MIR205HG (HGNC:43562): (MIR205 host gene)

MIR205 (HGNC:31583): (microRNA 205) 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR205HG	NR_145433.1	n.623_625dupGCA		non_coding_transcript_exon_variant	Exon 3 of 3
MIR205HG	NR_145434.1	n.758_760dupGCA		non_coding_transcript_exon_variant	Exon 5 of 5
MIR205HG	NR_145435.1	n.706_708dupGCA		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR205HG	ENST00000366437.8	n.677_679dupGCA		non_coding_transcript_exon_variant	Exon 4 of 4	3
MIR205HG	ENST00000429156.7	n.788_790dupGCA		non_coding_transcript_exon_variant	Exon 5 of 5	3
MIR205HG	ENST00000431096.7	n.709_711dupGCA		non_coding_transcript_exon_variant	Exon 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10235 AN: 149424 Hom.: 1121 Cov.: 0

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0194

Gnomad EAS AF: 0.0101

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.000290

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.00329

Gnomad OTH AF: 0.0554

GnomAD2 exomes AF: 0.0172 AC: 3340 AN: 194576 AF XY: 0.0148

Gnomad AFR exome AF: 0.177

Gnomad AMR exome AF: 0.0176

Gnomad ASJ exome AF: 0.0181

Gnomad EAS exome AF: 0.0114

Gnomad FIN exome AF: 0.000348

Gnomad NFE exome AF: 0.00333

Gnomad OTH exome AF: 0.0229

GnomAD4 exome AF: 0.00928 AC: 10980 AN: 1183418 Hom.: 455 Cov.: 0 AF XY: 0.00868 AC XY: 5080 AN XY: 585054

African (AFR) AF: 0.226 AC: 5836 AN: 25854

American (AMR) AF: 0.0171 AC: 581 AN: 34056

Ashkenazi Jewish (ASJ) AF: 0.0186 AC: 303 AN: 16278

East Asian (EAS) AF: 0.0137 AC: 225 AN: 16398

South Asian (SAS) AF: 0.00791 AC: 643 AN: 81266

European-Finnish (FIN) AF: 0.000666 AC: 20 AN: 30016

Middle Eastern (MID) AF: 0.0296 AC: 123 AN: 4158

European-Non Finnish (NFE) AF: 0.00258 AC: 2409 AN: 932502

Other (OTH) AF: 0.0196 AC: 840 AN: 42890

GnomAD4 genome AF: 0.0686 AC: 10259 AN: 149536 Hom.: 1124 Cov.: 0 AF XY: 0.0654 AC XY: 4773 AN XY: 72946

African (AFR) AF: 0.230 AC: 9255 AN: 40242

American (AMR) AF: 0.0325 AC: 489 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.0194 AC: 67 AN: 3456

East Asian (EAS) AF: 0.00993 AC: 50 AN: 5034

South Asian (SAS) AF: 0.0108 AC: 50 AN: 4630

European-Finnish (FIN) AF: 0.000290 AC: 3 AN: 10334

Middle Eastern (MID) AF: 0.0308 AC: 9 AN: 292

European-Non Finnish (NFE) AF: 0.00329 AC: 222 AN: 67528

Other (OTH) AF: 0.0548 AC: 114 AN: 2080

Alfa AF: 0.00842 Hom.: 2701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3842530; hg19: chr1-209605636; COSMIC: COSV63532160;