Variant 5-154685822-TA-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Variant links:

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]

LARP1 links:

MIR1303 (HGNC:):

MIR1303 links:

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ACMG classification

Classification made for transcript

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	Effect	Protein
LARP1	NM_001367713.1 linkuse as main transcript	c.-180+2788delA	intron_variant	NP_001354642.1
LARP1	NM_001367714.1 linkuse as main transcript	c.-297+2788delA	intron_variant	NP_001354643.1
LARP1	NM_001367716.1 linkuse as main transcript	c.-180+2788delA	intron_variant	NP_001354645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARP1	ENST00000687700.1 linkuse as main transcript	c.-180+2788delA		intron_variant				ENSP00000508958.1		A0A8I5KSP1
MIR1303	ENST00000408625.1 linkuse as main transcript	n.50delA		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

94445

AN:

149116

Hom.:

29755

Cov.:

show subpopulations

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.:

AF XY:

0.462

AC XY:

84716

AN XY:

183246

show subpopulations

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.:

AF XY:

0.633

AC XY:

46029

AN XY:

72728

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over