5-160485411-C-G

Position:

• chr5-160485411-C-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000517927.1(MIR3142HG):​n.286C>G 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 0.727 in 528,390 control chromosomes in the GnomAD database, including 141,782 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 0.70 (38097 hom., cov: 31)
  • Exomes 𝑓: 0.74 (103685 hom.)
• Consequence: MIR3142HG ENST00000517927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57

Genes affected

MIR3142HG (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR146A	NR_029701.1	n.60C>G		non_coding_transcript_exon_variant	1/1
MIR3142HG	NR_132748.1	n.303C>G		non_coding_transcript_exon_variant	2/2
MIR146A	unassigned_transcript_889	n.4C>G		non_coding_transcript_exon_variant	1/1
MIR146A	unassigned_transcript_888	n.*18C>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000517927.1	n.286C>G		non_coding_transcript_exon_variant	2/2	1
MIR146A	ENST00000385201.1	n.60C>G		non_coding_transcript_exon_variant	1/1	6
MIR3142HG	ENST00000642173.1	n.189C>G		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106630 AN: 151942 Hom.: 38071 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.687

GnomAD3 exomes AF: 0.713 AC: 175623 AN: 246292 Hom.: 64108 AF XY: 0.719 AC XY: 95733 AN XY: 133108

Gnomad AFR exome AF: 0.598

Gnomad AMR exome AF: 0.694

Gnomad ASJ exome AF: 0.777

Gnomad EAS exome AF: 0.372

Gnomad SAS exome AF: 0.720

Gnomad FIN exome AF: 0.784

Gnomad NFE exome AF: 0.770

Gnomad OTH exome AF: 0.730

GnomAD4 exome AF: 0.737 AC: 277348 AN: 376330 Hom.: 103685 Cov.: 0 AF XY: 0.738 AC XY: 157630 AN XY: 213566

Gnomad4 AFR exome AF: 0.599

Gnomad4 AMR exome AF: 0.694

Gnomad4 ASJ exome AF: 0.777

Gnomad4 EAS exome AF: 0.376

Gnomad4 SAS exome AF: 0.727

Gnomad4 FIN exome AF: 0.782

Gnomad4 NFE exome AF: 0.772

Gnomad4 OTH exome AF: 0.733

GnomAD4 genome AF: 0.702 AC: 106701 AN: 152060 Hom.: 38097 Cov.: 31 AF XY: 0.702 AC XY: 52221 AN XY: 74344

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.709

Gnomad4 ASJ AF: 0.783

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.688

Alfa AF: 0.755 Hom.: 14093

Bravo AF: 0.691

Asia WGS AF: 0.549 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	17
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2910164; hg19: chr5-159912418;