rs883517

chr5-160477722-T-C

Variant summary

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

The NR_132748.1(MIR3142HG):n.191-7577T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 151,970 control chromosomes in the GnomAD database, including 4,565 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 0.21 (4565 hom., cov: 32)
• Consequence: MIR3142HG NR_132748.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.939

Genes affected

MIR3142HG (HGNC:51944): (MIR3142 host gene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIR3142HG	NR_132748.1	n.191-7577T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR3142HG	ENST00000517927.1	n.174-7577T>C		intron_variant, non_coding_transcript_variant		1
MIR3142HG	ENST00000642173.1	n.77-7577T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32583 AN: 151852 Hom.: 4552 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.218

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.215 AC: 32627 AN: 151970 Hom.: 4565 Cov.: 32 AF XY: 0.214 AC XY: 15867 AN XY: 74288

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.217

Alfa AF: 0.140 Hom.: 2579

Bravo AF: 0.231

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	18
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs883517; hg19: chr5-159904729;