chr5-154685822-TA-T

Position:

• chr5-154685822-TA-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NR_031638.1(MIR1303):​n.50del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (29762 hom., cov: 0)
  • Exomes 𝑓: 0.46 (12830 hom.)
• Consequence: MIR1303 NR_031638.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

MIR1303 (HGNC:35301): (microRNA 1303) 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]

LARP1 (HGNC:29531): (La ribonucleoprotein 1, translational regulator) Enables eukaryotic initiation factor 4E binding activity; nucleic acid binding activity; and ribosomal small subunit binding activity. Involved in several processes, including TORC1 signaling; cellular response to rapamycin; and posttranscriptional regulation of gene expression. Located in cytoplasmic stress granule. Colocalizes with TORC1 complex and polysomal ribosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MIR1303	NR_031638.1	n.50del		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MIR1303	ENST00000408625.1	n.50del		non_coding_transcript_exon_variant	1/1
LARP1	ENST00000687700.1	c.-180+2788del		intron_variant				ENSP00000508958

Frequencies

GnomAD3 genomes AF: 0.633 AC: 94445 AN: 149116 Hom.: 29755 Cov.: 0

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.662

Gnomad OTH AF: 0.597

GnomAD4 exome AF: 0.458 AC: 145661 AN: 317870 Hom.: 12830 Cov.: 0 AF XY: 0.462 AC XY: 84716 AN XY: 183246

Gnomad4 AFR exome AF: 0.503

Gnomad4 AMR exome AF: 0.311

Gnomad4 ASJ exome AF: 0.448

Gnomad4 EAS exome AF: 0.446

Gnomad4 SAS exome AF: 0.448

Gnomad4 FIN exome AF: 0.504

Gnomad4 NFE exome AF: 0.482

Gnomad4 OTH exome AF: 0.472

GnomAD4 genome AF: 0.633 AC: 94497 AN: 149220 Hom.: 29762 Cov.: 0 AF XY: 0.633 AC XY: 46029 AN XY: 72728

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.662

Gnomad4 OTH AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs33982250; hg19: chr5-154065382;