rs1592749

Variant names:

• chr5-160545014-T-G
• rs1592749
• ENST00000770454.1:n.657+28786T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000770454.1(MIR3142HG):​n.657+28786T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,910 control chromosomes in the GnomAD database, including 38,361 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 (38361 hom., cov: 31)
• Consequence: MIR3142HG ENST00000770454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000770454.1	n.657+28786T>G		intron_variant	Intron 2 of 2
MIR3142HG	ENST00000770455.1	n.562+28786T>G		intron_variant	Intron 3 of 3
MIR3142HG	ENST00000770456.1	n.287-7526T>G		intron_variant	Intron 2 of 3
MIR3142HG	ENST00000770457.1	n.264-7526T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106971 AN: 151792 Hom.: 38299 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.705 AC: 107096 AN: 151910 Hom.: 38361 Cov.: 31 AF XY: 0.710 AC XY: 52680 AN XY: 74224

African (AFR) AF: 0.792 AC: 32830 AN: 41450

American (AMR) AF: 0.758 AC: 11583 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3470

East Asian (EAS) AF: 0.990 AC: 5138 AN: 5188

South Asian (SAS) AF: 0.793 AC: 3810 AN: 4806

European-Finnish (FIN) AF: 0.612 AC: 6419 AN: 10482

Middle Eastern (MID) AF: 0.670 AC: 193 AN: 288

European-Non Finnish (NFE) AF: 0.629 AC: 42699 AN: 67930

Other (OTH) AF: 0.697 AC: 1473 AN: 2112

Alfa AF: 0.688 Hom.: 29553

Bravo AF: 0.721

Asia WGS AF: 0.898 AC: 3121 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.6
DANN	Benign	0.38
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs1592749; hg19: chr5-159972021;