12-94834510-G-C

Variant names:

• chr12-94834510-G-C
• rs2289030
• ENST00000405395.2:n.57G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_030171.1(MIR492):​n.113G>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0819 in 556,072 control chromosomes in the GnomAD database, including 2,721 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 0.067 (575 hom., cov: 33)
  • Exomes 𝑓: 0.088 (2146 hom.)
• Consequence: MIR492 NR_030171.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.04
• Publications: 58 publications found

Genes affected

KRT19P2 (HGNC:):

KRT19P2 (HGNC:33423): (keratin 19 pseudogene 2)

MIR492 (HGNC:32081): (microRNA 492) 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_030171.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR492	NR_030171.1		n.113G>C		non_coding_transcript_exon	Exon 1 of 1
	KRT19P2	NR_036685.1		n.57G>C		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KRT19P2	ENST00000405395.2	TSL:6	n.57G>C		non_coding_transcript_exon	Exon 1 of 1
	KRT19P2	ENST00000557173.1	TSL:6	n.364G>C		non_coding_transcript_exon	Exon 1 of 1
	MIR492	ENST00000638676.1	TSL:6	n.113G>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10185 AN: 152184 Hom.: 573 Cov.: 33

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0742

GnomAD2 exomes AF: 0.0974 AC: 24464 AN: 251230 AF XY: 0.0939

Gnomad AFR exome AF: 0.0161

Gnomad AMR exome AF: 0.191

Gnomad ASJ exome AF: 0.0741

Gnomad EAS exome AF: 0.246

Gnomad FIN exome AF: 0.102

Gnomad NFE exome AF: 0.0579

Gnomad OTH exome AF: 0.0885

GnomAD4 exome AF: 0.0876 AC: 35365 AN: 403770 Hom.: 2146 Cov.: 0 AF XY: 0.0858 AC XY: 19657 AN XY: 229082

African (AFR) AF: 0.0180 AC: 199 AN: 11062

American (AMR) AF: 0.190 AC: 7032 AN: 36948

Ashkenazi Jewish (ASJ) AF: 0.0719 AC: 901 AN: 12540

East Asian (EAS) AF: 0.238 AC: 3592 AN: 15072

South Asian (SAS) AF: 0.0974 AC: 6607 AN: 67834

European-Finnish (FIN) AF: 0.0984 AC: 3310 AN: 33638

Middle Eastern (MID) AF: 0.0557 AC: 145 AN: 2602

European-Non Finnish (NFE) AF: 0.0588 AC: 12112 AN: 205908

Other (OTH) AF: 0.0808 AC: 1467 AN: 18166

GnomAD4 genome AF: 0.0670 AC: 10198 AN: 152302 Hom.: 575 Cov.: 33 AF XY: 0.0725 AC XY: 5400 AN XY: 74468

African (AFR) AF: 0.0173 AC: 721 AN: 41592

American (AMR) AF: 0.136 AC: 2076 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0796 AC: 276 AN: 3468

East Asian (EAS) AF: 0.247 AC: 1276 AN: 5172

South Asian (SAS) AF: 0.102 AC: 491 AN: 4828

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10602

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4081 AN: 68026

Other (OTH) AF: 0.0729 AC: 154 AN: 2112

Alfa AF: 0.0492 Hom.: 79

Bravo AF: 0.0679

Asia WGS AF: 0.135 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.8
DANN	Benign	0.54
PhyloP100		5.0

Splicing

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

Other links and lift over

dbSNP: rs2289030; hg19: chr12-95228286;