Genetic Variant KRT19P2:n.57G>C (chr12-94834510-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.04

Variant links:

Genes affected

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

KRT19P2 links:

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]

MIR492 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
MIR492	NR_030171.1 link	n.113G>C	non_coding_transcript_exon_variant	Exon 1 of 1
KRT19P2	NR_036685.1 link	n.57G>C	non_coding_transcript_exon_variant	Exon 1 of 1
MIR492	unassigned_transcript_2047	n.*61G>C	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
KRT19P2	ENST00000405395.2 link	n.57G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
KRT19P2	ENST00000557173.1 link	n.364G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
MIR492	ENST00000638676.1 link	n.113G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes

AF:

0.0669

AC:

10185

AN:

152184

Hom.:

573

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.0974

AC:

24464

AN:

251230

Hom.:

1713

AF XY:

0.0939

AC XY:

12760

AN XY:

135840

show subpopulations

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 SAS exome

AF:

0.0987

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.:

AF XY:

0.0858

AC XY:

19657

AN XY:

229082

show subpopulations

Gnomad4 AFR exome

AF:

0.0180

Gnomad4 AMR exome

AF:

0.190

Gnomad4 ASJ exome

AF:

0.0719

Gnomad4 EAS exome

AF:

0.238

Gnomad4 SAS exome

AF:

0.0974

Gnomad4 FIN exome

AF:

0.0984

Gnomad4 NFE exome

AF:

0.0588

Gnomad4 OTH exome

AF:

0.0808

GnomAD4 genome

AF:

0.0670

AC:

10198

AN:

152302

Hom.:

575

Cov.:

AF XY:

0.0725

AC XY:

5400

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.0173

Gnomad4 AMR

AF:

0.136

Gnomad4 ASJ

AF:

0.0796

Gnomad4 EAS

AF:

0.247

Gnomad4 SAS

AF:

0.102

Gnomad4 FIN

AF:

0.105

Gnomad4 NFE

AF:

0.0600

Gnomad4 OTH

AF:

0.0729

Alfa

AF:

0.0492

Hom.:

Bravo

AF:

0.0679

Asia WGS

AF:

0.135

AC:

466

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

3.8

DANN

Benign

0.54

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over