chrX-145994784-T-A

Variant names:

• chrX-145994784-T-A
• rs5965660
• ENST00000401186.1:n.77A>T

Variant summary

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

The ENST00000401186.1(MIR888):​n.77A>T variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 268,846 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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: 23)
  • Exomes 𝑓: 0.0000037 (0 hom. 0 hem.)
• Consequence: MIR888 ENST00000401186.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 13 publications found

Genes affected

MIR888 (HGNC:33648): (microRNA 888) 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
MIR888	NR_030592.1	n.77A>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1
MIR888	unassigned_transcript_3835	n.*10A>T		downstream_gene_variant
MIR888	unassigned_transcript_3836	n.*46A>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MIR888	ENST00000401186.1	n.77A>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD2 exomes AF: 0.00000581 AC: 1 AN: 172252 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000373

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000372 AC: 1 AN: 268846 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 105026

African (AFR) AF: 0.00 AC: 0 AN: 8325

American (AMR) AF: 0.0000352 AC: 1 AN: 28431

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 8529

East Asian (EAS) AF: 0.00 AC: 0 AN: 9721

South Asian (SAS) AF: 0.00 AC: 0 AN: 39140

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 24074

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2043

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 136415

Other (OTH) AF: 0.00 AC: 0 AN: 12168

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.58
DANN	Benign	0.49
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5965660; hg19: chrX-145076302;