rs6864584

Variant names:

• chr5-160467978-T-C
• rs6864584
• ENST00000770454.1:n.74T>C

Variant summary

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

The ENST00000770454.1(MIR3142HG):​n.74T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 152,166 control chromosomes in the GnomAD database, including 841 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 0.060 (841 hom., cov: 33)
• Consequence: MIR3142HG ENST00000770454.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 9 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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR3142HG	ENST00000770454.1		n.74T>C		non_coding_transcript_exon	Exon 1 of 3
	MIR3142HG	ENST00000770459.1		n.152T>C		non_coding_transcript_exon	Exon 1 of 1
	MIR3142HG	ENST00000642173.1		n.77-17321T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0599 AC: 9106 AN: 152048 Hom.: 840 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.0429

Gnomad FIN AF: 0.000754

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00278

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0600 AC: 9125 AN: 152166 Hom.: 841 Cov.: 33 AF XY: 0.0596 AC XY: 4435 AN XY: 74414

African (AFR) AF: 0.194 AC: 8045 AN: 41492

American (AMR) AF: 0.0245 AC: 375 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5174

South Asian (SAS) AF: 0.0423 AC: 204 AN: 4822

European-Finnish (FIN) AF: 0.000754 AC: 8 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00278 AC: 189 AN: 67994

Other (OTH) AF: 0.0469 AC: 99 AN: 2112

Alfa AF: 0.0359 Hom.: 67

Bravo AF: 0.0668

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	10
DANN	Benign	0.61
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs6864584; hg19: chr5-159894985;