rs57095329

Positions:

• chr5-160467840-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000642173.1(MIR3142HG):​n.77-17459A>G variant causes a intron, non coding transcript 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 ENST00000642173.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.901

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR3142HG	ENST00000642173.1	n.77-17459A>G		intron_variant, non_coding_transcript_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

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0486 Hom.: 56

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57095329; hg19: chr5-159894847;