ENST00000692840.2:n.592T>A

Variant names:

• chr6-33208047-A-T
• rs213210
• ENST00000692840.2:n.592T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000692840.2(ENSG00000288751):​n.592T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288751 ENST00000692840.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 66 publications found

Genes affected

ENSG00000288751 (HGNC:):

MIR219A1 (HGNC:31597): (microRNA 219a-1) 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000692840.2. 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
	MIR219A1	NR_029633.1		n.*103A>T		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288751	ENST00000692840.2		n.592T>A		non_coding_transcript_exon	Exon 1 of 1
	MIR219A1	ENST00000362166.1	TSL:6	n.*103A>T		downstream_gene	N/A
	ENSG00000306895	ENST00000821858.1		n.*193A>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 182532 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 103866

African (AFR) AF: 0.00 AC: 0 AN: 4880

American (AMR) AF: 0.00 AC: 0 AN: 9554

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5042

East Asian (EAS) AF: 0.00 AC: 0 AN: 8090

South Asian (SAS) AF: 0.00 AC: 0 AN: 34638

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21438

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1456

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 89214

Other (OTH) AF: 0.00 AC: 0 AN: 8220

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.70
DANN	Benign	0.47
PhyloP100		-1.3
PromoterAI		0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs213210; hg19: chr6-33175824;