chr1-209432291-TAGCAGCAGC-T

Variant names:

• chr1-209432291-TAGCAGCAGC-T
• rs3842530
• ENST00000366437.8:n.671_679delGCAGCAGCA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000366437.8(MIR205HG):​n.671_679delGCAGCAGCA 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 0.000727 in 1,333,090 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0021 (2 hom., cov: 0)
  • Exomes 𝑓: 0.00055 (1 hom.)
• Consequence: MIR205HG ENST00000366437.8 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.825
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366437.8. 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
	MIR205HG	NR_145433.1		n.617_625delGCAGCAGCA		non_coding_transcript_exon	Exon 3 of 3
	MIR205HG	NR_145434.1		n.752_760delGCAGCAGCA		non_coding_transcript_exon	Exon 5 of 5
	MIR205HG	NR_145435.1		n.700_708delGCAGCAGCA		non_coding_transcript_exon	Exon 4 of 4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR205HG	ENST00000366437.8	TSL:3	n.671_679delGCAGCAGCA		non_coding_transcript_exon	Exon 4 of 4
	MIR205HG	ENST00000429156.7	TSL:3	n.782_790delGCAGCAGCA		non_coding_transcript_exon	Exon 5 of 5
	MIR205HG	ENST00000431096.7	TSL:3	n.703_711delGCAGCAGCA		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.00214 AC: 320 AN: 149468 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00627

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00113

Gnomad ASJ AF: 0.000290

Gnomad EAS AF: 0.00258

Gnomad SAS AF: 0.000863

Gnomad FIN AF: 0.0000968

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000474

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000548 AC: 648 AN: 1183512 Hom.: 1 AF XY: 0.000545 AC XY: 319 AN XY: 585112

African (AFR) AF: 0.00676 AC: 175 AN: 25904

American (AMR) AF: 0.000851 AC: 29 AN: 34060

Ashkenazi Jewish (ASJ) AF: 0.0000614 AC: 1 AN: 16278

East Asian (EAS) AF: 0.00219 AC: 36 AN: 16402

South Asian (SAS) AF: 0.000984 AC: 80 AN: 81278

European-Finnish (FIN) AF: 0.000133 AC: 4 AN: 30014

Middle Eastern (MID) AF: 0.00144 AC: 6 AN: 4160

European-Non Finnish (NFE) AF: 0.000290 AC: 270 AN: 932514

Other (OTH) AF: 0.00110 AC: 47 AN: 42902

GnomAD4 genome AF: 0.00215 AC: 321 AN: 149578 Hom.: 2 Cov.: 0 AF XY: 0.00207 AC XY: 151 AN XY: 72966

African (AFR) AF: 0.00628 AC: 253 AN: 40276

American (AMR) AF: 0.00113 AC: 17 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.000290 AC: 1 AN: 3454

East Asian (EAS) AF: 0.00258 AC: 13 AN: 5034

South Asian (SAS) AF: 0.000864 AC: 4 AN: 4630

European-Finnish (FIN) AF: 0.0000968 AC: 1 AN: 10334

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000474 AC: 32 AN: 67532

Other (OTH) AF: 0.00 AC: 0 AN: 2080

Alfa AF: 0.00 Hom.: 2701

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.82
Mutation Taster		=97/3	polymorphism

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: COSV63532449;