rs11671784

chr19-13836482-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_029501.1(MIR27A):n.36C>T 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 0.0123 in 539,264 control chromosomes in the GnomAD database, including 66 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 0.012 (18 hom., cov: 32)
  • Exomes 𝑓: 0.013 (48 hom.)
• Consequence: MIR27A NR_029501.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948

Genes affected

MIR27A (HGNC:31613): (microRNA 27a) 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]

MIR23AHG (HGNC:27620): (miR-23a/27a/24-2 cluster host gene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0115 (1755/152338) while in subpopulation NFE AF= 0.0182 (1235/68024). AF 95% confidence interval is 0.0173. There are 18 homozygotes in gnomad4. There are 821 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 18 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR27A	NR_029501.1	n.36C>T		non_coding_transcript_exon_variant	1/1
MIR23AHG	NR_036515.2	n.6437C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR27A	ENST00000385073.1	n.36C>T		non_coding_transcript_exon_variant	1/1
MIR23AHG	ENST00000587762.2	n.6447C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0115 AC: 1752 AN: 152222 Hom.: 18 Cov.: 32

Gnomad AFR AF: 0.00343

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0177

GnomAD3 exomes AF: 0.0119 AC: 2918 AN: 245456 Hom.: 25 AF XY: 0.0121 AC XY: 1612 AN XY: 132826

Gnomad AFR exome AF: 0.00279

Gnomad AMR exome AF: 0.00867

Gnomad ASJ exome AF: 0.0337

Gnomad EAS exome AF: 0.0000551

Gnomad SAS exome AF: 0.00503

Gnomad FIN exome AF: 0.00214

Gnomad NFE exome AF: 0.0176

Gnomad OTH exome AF: 0.0168

GnomAD4 exome AF: 0.0126 AC: 4860 AN: 386926 Hom.: 48 Cov.: 0 AF XY: 0.0124 AC XY: 2719 AN XY: 219826

Gnomad4 AFR exome AF: 0.00263

Gnomad4 AMR exome AF: 0.00874

Gnomad4 ASJ exome AF: 0.0347

Gnomad4 EAS exome AF: 0.0000718

Gnomad4 SAS exome AF: 0.00544

Gnomad4 FIN exome AF: 0.00285

Gnomad4 NFE exome AF: 0.0171

Gnomad4 OTH exome AF: 0.0141

GnomAD4 genome AF: 0.0115 AC: 1755 AN: 152338 Hom.: 18 Cov.: 32 AF XY: 0.0110 AC XY: 821 AN XY: 74490

Gnomad4 AFR AF: 0.00342

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00414

Gnomad4 FIN AF: 0.00179

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0180

Alfa AF: 0.0164 Hom.: 15

Bravo AF: 0.0118

Asia WGS AF: 0.00346 AC: 12 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	15
Dann	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11671784; hg19: chr19-13947296;