chr20-26208276-A-C

Position:

• chr20-26208276-A-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_030386.1(MIR663A):​n.3T>G variant causes a non coding transcript exon 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: 𝑓 0.0018 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00014 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MIR663A NR_030386.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR663A	NR_030386.1	n.3T>G		non_coding_transcript_exon_variant	1/1
MIR663AHG	NR_040095.1	n.111+847T>G		intron_variant
MIR663A	unassigned_transcript_3435	n.-12T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR663AHG	ENST00000427348.5	n.111+847T>G		intron_variant		1
MIR663A	ENST00000385250.1	n.3T>G		non_coding_transcript_exon_variant	1/1	6
MIR663AHG	ENST00000432499.6	n.41+723T>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00176 AC: 103 AN: 58460 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000511

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00143

Gnomad ASJ AF: 0.00515

Gnomad EAS AF: 0.00243

Gnomad SAS AF: 0.00254

Gnomad FIN AF: 0.00165

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00291

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000138 AC: 19 AN: 138038 Hom.: 0 Cov.: 0 AF XY: 0.000122 AC XY: 10 AN XY: 82282

Gnomad4 AFR exome AF: 0.000417

Gnomad4 AMR exome AF: 0.000395

Gnomad4 ASJ exome AF: 0.000175

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000966

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000136

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00176 AC: 103 AN: 58516 Hom.: 0 Cov.: 0 AF XY: 0.00178 AC XY: 51 AN XY: 28622

Gnomad4 AFR AF: 0.000509

Gnomad4 AMR AF: 0.00143

Gnomad4 ASJ AF: 0.00515

Gnomad4 EAS AF: 0.00243

Gnomad4 SAS AF: 0.00254

Gnomad4 FIN AF: 0.00165

Gnomad4 NFE AF: 0.00291

Gnomad4 OTH AF: 0.00

Alfa AF: 0.508 Hom.: 5412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7266947; hg19: chr20-26188912; COSMIC: COSV101155723;