rs73056059

Variant names:

• chr19-49501100-G-A
• rs73056059
• ENST00000385048.3:n.-232C>T

Your query was ambiguous. Multiple possible variants found:

• chr19-49501100-G-A
• chr19-49501100-G-C

Variant summary

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

The NR_029703.1(MIR150):​n.-232C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,150 control chromosomes in the GnomAD database, including 3,663 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 0.18 (3663 hom., cov: 32)
• Consequence: MIR150 NR_029703.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.30
• Publications: 7 publications found

Genes affected

MIR150 (HGNC:31537): (microRNA 150) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_029703.1. 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
	MIR150	NR_029703.1		n.-232C>T		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIR150	ENST00000385048.3	TSL:6	n.-232C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27760 AN: 152032 Hom.: 3655 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.167

GnomAD2 exomes AF: 0.114 AC: 91 AN: 800 AF XY: 0.105

Gnomad AFR exome AF: 0.389

Gnomad AMR exome AF: 0.0604

Gnomad ASJ exome AF: 0.300

Gnomad EAS exome AF: 0.0208

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.100

Gnomad OTH exome AF: 0.0909

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

GnomAD4 genome AF: 0.183 AC: 27802 AN: 152150 Hom.: 3663 Cov.: 32 AF XY: 0.179 AC XY: 13299 AN XY: 74378

African (AFR) AF: 0.372 AC: 15435 AN: 41460

American (AMR) AF: 0.134 AC: 2053 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0916 AC: 318 AN: 3472

East Asian (EAS) AF: 0.0645 AC: 334 AN: 5176

South Asian (SAS) AF: 0.104 AC: 500 AN: 4820

European-Finnish (FIN) AF: 0.0920 AC: 976 AN: 10614

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7627 AN: 67996

Other (OTH) AF: 0.167 AC: 354 AN: 2116

Alfa AF: 0.162 Hom.: 620

Bravo AF: 0.194

Asia WGS AF: 0.128 AC: 446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		2.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs73056059; hg19: chr19-50004357;