rs57095329

Variant names:

• chr5-160467840-A-G
• rs57095329
• ENST00000770459.1:n.14A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000770459.1(MIR3142HG):​n.14A>G 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 0.0792 in 152,300 control chromosomes in the GnomAD database, including 773 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 0.079 (773 hom., cov: 33)
• Consequence: MIR3142HG ENST00000770459.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901
• Publications: 102 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.182 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	ENST00000770459.1	n.14A>G		non_coding_transcript_exon_variant	Exon 1 of 1
MIR3142HG	ENST00000642173.1	n.77-17459A>G		intron_variant	Intron 1 of 1
MIR3142HG	ENST00000770454.1	n.-65A>G		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0791 AC: 12033 AN: 152182 Hom.: 770 Cov.: 33

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0779

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

GnomAD4 genome AF: 0.0792 AC: 12067 AN: 152300 Hom.: 773 Cov.: 33 AF XY: 0.0823 AC XY: 6128 AN XY: 74460

African (AFR) AF: 0.152 AC: 6331 AN: 41564

American (AMR) AF: 0.108 AC: 1659 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3468

East Asian (EAS) AF: 0.192 AC: 993 AN: 5184

South Asian (SAS) AF: 0.131 AC: 633 AN: 4820

European-Finnish (FIN) AF: 0.0361 AC: 383 AN: 10610

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0271 AC: 1841 AN: 68024

Other (OTH) AF: 0.0814 AC: 172 AN: 2114

Alfa AF: 0.0471 Hom.: 479

Bravo AF: 0.0864

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs57095329; hg19: chr5-159894847;