rs73318382

Variant names:

• chr5-160467536-A-C
• rs73318382
• ENST00000642173.1:n.77-17763A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642173.1(MIR3142HG):​n.77-17763A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 152,138 control chromosomes in the GnomAD database, including 403 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 0.057 (403 hom., cov: 32)
• Consequence: MIR3142HG ENST00000642173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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	ENST00000642173.1	n.77-17763A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8609 AN: 152020 Hom.: 400 Cov.: 32

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0362

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0268

Gnomad OTH AF: 0.0569

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

GnomAD4 genome AF: 0.0567 AC: 8631 AN: 152138 Hom.: 403 Cov.: 32 AF XY: 0.0601 AC XY: 4469 AN XY: 74368

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0362

Gnomad4 NFE AF: 0.0268

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0462 Hom.: 25

Bravo AF: 0.0606

Asia WGS AF: 0.178 AC: 617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73318382; hg19: chr5-159894543;