3-67225635-G-T

Variant names:

• chr3-67225635-G-T
• rs9868022
• ENST00000635924.1:n.*108G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_036234.1(MIR4272):​n.*108G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 153,476 control chromosomes in the GnomAD database, including 69,502 homozygotes. 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 0.95 (68957 hom., cov: 33)
  • Exomes 𝑓: 0.97 (545 hom.)
• Consequence: MIR4272 NR_036234.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670

Genes affected

MIR4272 (HGNC:38303): (microRNA 4272) 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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MIR4272	NR_036234.1	n.*108G>T		downstream_gene_variant
MIR4272	unassigned_transcript_639	n.*118G>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR4272	ENST00000635924.1	n.*108G>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144674 AN: 152200 Hom.: 68896 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.926

Gnomad ASJ AF: 0.928

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.945

GnomAD4 exome AF: 0.971 AC: 1123 AN: 1156 Hom.: 545 AF XY: 0.974 AC XY: 641 AN XY: 658

Gnomad4 AFR exome AF: 0.844

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.991

Gnomad4 NFE exome AF: 0.973

Gnomad4 OTH exome AF: 0.933

GnomAD4 genome AF: 0.951 AC: 144795 AN: 152320 Hom.: 68957 Cov.: 33 AF XY: 0.953 AC XY: 70948 AN XY: 74470

Gnomad4 AFR AF: 0.899

Gnomad4 AMR AF: 0.926

Gnomad4 ASJ AF: 0.928

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.987

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.946

Alfa AF: 0.955 Hom.: 11721

Bravo AF: 0.940

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9868022; hg19: chr3-67276059;