ENST00000595160.2:n.56T>A

Variant names:

• chr19-53788157-A-T
• rs3859501
• ENST00000595160.2:n.56T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000595160.2(ENSG00000269877):​n.56T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000269877 ENST00000595160.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 12 publications found

Genes affected

ENSG00000269877 (HGNC:):

MIR372 (HGNC:31786): (microRNA 372) 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904767	XR_007067336.1	n.69T>A		non_coding_transcript_exon_variant	Exon 1 of 2
MIR372	NR_029865.1	n.*201A>T		downstream_gene_variant
MIR372	unassigned_transcript_3400	n.*240A>T		downstream_gene_variant
MIR372	unassigned_transcript_3401	n.*204A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000269877	ENST00000595160.2	n.56T>A		non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000269877	ENST00000775521.1	n.45T>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000269564	ENST00000597420.2	n.90-440A>T		intron_variant	Intron 1 of 1	6
MIR372	ENST00000362225.1	n.*201A>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 104112 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 56682

African (AFR) AF: 0.00 AC: 0 AN: 3360

American (AMR) AF: 0.00 AC: 0 AN: 6550

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2238

East Asian (EAS) AF: 0.00 AC: 0 AN: 5544

South Asian (SAS) AF: 0.00 AC: 0 AN: 20240

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4476

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 56520

Other (OTH) AF: 0.00 AC: 0 AN: 4872

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 35070

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs3859501; hg19: chr19-54291411;