rs12514981

Variant names:

• chr5-160546827-T-C
• rs12514981
• ENST00000770454.1:n.657+30599T>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+30599T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0531 in 152,234 control chromosomes in the GnomAD database, including 287 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 0.053 (287 hom., cov: 32)
• Consequence: MIR3142HG ENST00000770454.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.0798 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+30599T>C		intron_variant	Intron 2 of 2
MIR3142HG	ENST00000770455.1	n.562+30599T>C		intron_variant	Intron 3 of 3
MIR3142HG	ENST00000770456.1	n.287-5713T>C		intron_variant	Intron 2 of 3
MIR3142HG	ENST00000770457.1	n.264-5713T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8079 AN: 152116 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0531 AC: 8077 AN: 152234 Hom.: 287 Cov.: 32 AF XY: 0.0510 AC XY: 3795 AN XY: 74428

African (AFR) AF: 0.0147 AC: 609 AN: 41546

American (AMR) AF: 0.0540 AC: 826 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0249 AC: 120 AN: 4814

European-Finnish (FIN) AF: 0.0457 AC: 485 AN: 10602

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0816 AC: 5551 AN: 68008

Other (OTH) AF: 0.0630 AC: 133 AN: 2110

Alfa AF: 0.0732 Hom.: 377

Bravo AF: 0.0528

Asia WGS AF: 0.0130 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.76
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs12514981; hg19: chr5-159973834;