chr12-94834510-G-C

Position:

• chr12-94834510-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KRT19P2 (HGNC:):

ACMG classification

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	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR492	NR_030171.1	n.113G>C		non_coding_transcript_exon_variant	1/1
KRT19P2	NR_036685.1	n.57G>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KRT19P2	ENST00000405395.2	n.57G>C		non_coding_transcript_exon_variant	1/1	6
KRT19P2	ENST00000557173.1	n.364G>C		non_coding_transcript_exon_variant	1/1	6
MIR492	ENST00000638676.1	n.113G>C		non_coding_transcript_exon_variant	1/1	6

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

GnomAD3 exomes AF: 0.0974 AC: 24464 AN: 251230 Hom.: 1713 AF XY: 0.0939 AC XY: 12760 AN XY: 135840

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.: 0 AF XY: 0.0858 AC XY: 19657 AN XY: 229082

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.: 33 AF XY: 0.0725 AC XY: 5400 AN XY: 74468

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.: 79

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

Other links and lift over

dbSNP: rs2289030; hg19: chr12-95228286;