5-154685822-TAA-TA

Variant names:

• chr5-154685822-TA-T
• rs33982250
• NM_001367713.1:c.-180+2788delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001367713.1(LARP1):​c.-180+2788delA variant causes a intron 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: LARP1 NM_001367713.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

Genes affected

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]

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]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367713.1. 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
	LARP1	NM_001367713.1		c.-180+2788delA		intron	N/A	NP_001354642.1
	LARP1	NM_001367714.1		c.-297+2788delA		intron	N/A	NP_001354643.1
	LARP1	NM_001367716.1		c.-180+2788delA		intron	N/A	NP_001354645.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP1	ENST00000687700.1		c.-180+2788delA		intron	N/A	ENSP00000508958.1
	MIR1303	ENST00000408625.1	TSL:6	n.50delA		non_coding_transcript_exon	Exon 1 of 1

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

GnomAD2 exomes AF: 0.461 AC: 84201 AN: 182604 AF XY: 0.464

Gnomad AFR exome AF: 0.515

Gnomad AMR exome AF: 0.326

Gnomad ASJ exome AF: 0.452

Gnomad EAS exome AF: 0.464

Gnomad FIN exome AF: 0.509

Gnomad NFE exome AF: 0.490

Gnomad OTH exome AF: 0.469

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

African (AFR) AF: 0.503 AC: 3809 AN: 7576

American (AMR) AF: 0.311 AC: 9480 AN: 30472

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 4619 AN: 10320

East Asian (EAS) AF: 0.446 AC: 4946 AN: 11088

South Asian (SAS) AF: 0.448 AC: 25989 AN: 57998

European-Finnish (FIN) AF: 0.504 AC: 7505 AN: 14884

Middle Eastern (MID) AF: 0.523 AC: 1367 AN: 2614

European-Non Finnish (NFE) AF: 0.482 AC: 81158 AN: 168522

Other (OTH) AF: 0.472 AC: 6788 AN: 14396

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

African (AFR) AF: 0.643 AC: 25917 AN: 40298

American (AMR) AF: 0.504 AC: 7584 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2059 AN: 3450

East Asian (EAS) AF: 0.575 AC: 2918 AN: 5076

South Asian (SAS) AF: 0.611 AC: 2893 AN: 4732

European-Finnish (FIN) AF: 0.646 AC: 6477 AN: 10026

Middle Eastern (MID) AF: 0.587 AC: 168 AN: 286

European-Non Finnish (NFE) AF: 0.662 AC: 44566 AN: 67340

Other (OTH) AF: 0.596 AC: 1233 AN: 2068

Alfa AF: 0.475 Hom.: 999

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs33982250; hg19: chr5-154065382;