18-58451126-C-T

Position:

• chr18-58451126-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4 BS2

The ENST00000590797.4(MIR122HG):​n.1913C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0064 in 518,710 control chromosomes in the GnomAD database, including 27 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 0.0065 (8 hom., cov: 32)
  • Exomes 𝑓: 0.0063 (19 hom.)
• Consequence: MIR122HG ENST00000590797.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.03

Genes affected

MIR122 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR122	NR_029667.1	n.53C>T		non_coding_transcript_exon_variant	1/1
MIR3591	NR_039899.1	n.27G>A		non_coding_transcript_exon_variant	1/1
MIR122HG	NR_170244.1	n.453C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR122	ENST00000385044.3	n.53C>T		non_coding_transcript_exon_variant	1/1	6
MIR122HG	ENST00000590797.4	n.1913C>T		non_coding_transcript_exon_variant	2/2	2
MIR3591	ENST00000636727.1	n.27G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.00655 AC: 997 AN: 152162 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00215

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.00386

Gnomad ASJ AF: 0.00317

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00932

Gnomad OTH AF: 0.00622

GnomAD3 exomes AF: 0.00584 AC: 1327 AN: 227340 Hom.: 20 AF XY: 0.00575 AC XY: 703 AN XY: 122204

Gnomad AFR exome AF: 0.00146

Gnomad AMR exome AF: 0.00207

Gnomad ASJ exome AF: 0.00203

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000286

Gnomad FIN exome AF: 0.0110

Gnomad NFE exome AF: 0.00982

Gnomad OTH exome AF: 0.00352

GnomAD4 exome AF: 0.00634 AC: 2324 AN: 366430 Hom.: 19 Cov.: 0 AF XY: 0.00586 AC XY: 1219 AN XY: 208082

Gnomad4 AFR exome AF: 0.00213

Gnomad4 AMR exome AF: 0.00209

Gnomad4 ASJ exome AF: 0.00187

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000465

Gnomad4 FIN exome AF: 0.0102

Gnomad4 NFE exome AF: 0.00963

Gnomad4 OTH exome AF: 0.00626

GnomAD4 genome AF: 0.00655 AC: 997 AN: 152280 Hom.: 8 Cov.: 32 AF XY: 0.00685 AC XY: 510 AN XY: 74456

Gnomad4 AFR AF: 0.00214

Gnomad4 AMR AF: 0.00386

Gnomad4 ASJ AF: 0.00317

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.00932

Gnomad4 OTH AF: 0.00616

Alfa AF: 0.00763 Hom.: 5

Bravo AF: 0.00621

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	22
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41292412; hg19: chr18-56118358;