5-160542448-T-C

Variant names:

• chr5-160542448-T-C
• rs4301261
• ENST00000770454.1:n.657+26220T>C

Variant summary

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

The ENST00000770454.1(MIR3142HG):​n.657+26220T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,044 control chromosomes in the GnomAD database, including 25,635 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 0.57 (25635 hom., cov: 32)
• Consequence: MIR3142HG ENST00000770454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000770454.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3142HG	ENST00000770454.1		n.657+26220T>C		intron	N/A
	MIR3142HG	ENST00000770455.1		n.562+26220T>C		intron	N/A
	MIR3142HG	ENST00000770456.1		n.287-10092T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86721 AN: 151926 Hom.: 25613 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.571 AC: 86787 AN: 152044 Hom.: 25635 Cov.: 32 AF XY: 0.578 AC XY: 42931 AN XY: 74322

African (AFR) AF: 0.410 AC: 17010 AN: 41466

American (AMR) AF: 0.693 AC: 10580 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2199 AN: 3470

East Asian (EAS) AF: 0.864 AC: 4470 AN: 5172

South Asian (SAS) AF: 0.711 AC: 3427 AN: 4818

European-Finnish (FIN) AF: 0.592 AC: 6260 AN: 10576

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40882 AN: 67964

Other (OTH) AF: 0.584 AC: 1235 AN: 2114

Alfa AF: 0.600 Hom.: 23134

Bravo AF: 0.572

Asia WGS AF: 0.771 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.71
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs4301261; hg19: chr5-159969455;