20-26208276-A-G

Variant names:

• chr20-26208276-A-G
• rs7266947
• ENST00000427348.5:n.111+847T>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000427348.5(MIR663AHG):​n.111+847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 0)
  • Exomes 𝑓: 0.000014 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR663AHG ENST00000427348.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 9 publications found

Genes affected

MIR663AHG (HGNC:27662): (MIR663A host gene)

MIR663A (HGNC:32919): (microRNA 663a) 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.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427348.5. 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
	MIR663A	NR_030386.1		n.3T>C		non_coding_transcript_exon	Exon 1 of 1
	MIR663AHG	NR_040095.1		n.111+847T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR663AHG	ENST00000427348.5	TSL:1	n.111+847T>C		intron	N/A
	MIR663A	ENST00000385250.1	TSL:6	n.3T>C		non_coding_transcript_exon	Exon 1 of 1
	MIR663AHG	ENST00000432499.6	TSL:5	n.41+723T>C		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000144 AC: 2 AN: 138556 Hom.: 0 Cov.: 0 AF XY: 0.0000242 AC XY: 2 AN XY: 82614

African (AFR) AF: 0.00 AC: 0 AN: 2400

American (AMR) AF: 0.0000984 AC: 1 AN: 10166

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5738

East Asian (EAS) AF: 0.00 AC: 0 AN: 1252

South Asian (SAS) AF: 0.00 AC: 0 AN: 31132

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6834

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 994

European-Non Finnish (NFE) AF: 0.0000136 AC: 1 AN: 73798

Other (OTH) AF: 0.00 AC: 0 AN: 6242

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 5508

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	7.1
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7266947; hg19: chr20-26188912;