rs1870687

Positions:

• chr4-128138260-A-G
• chr4-128138260-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018078.4(LARP1B):​c.1524+16072A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,934 control chromosomes in the GnomAD database, including 27,714 homozygotes. 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: 𝑓 0.59 (27714 hom., cov: 31)
• Consequence: LARP1B NM_018078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

LARP1B (HGNC:24704): (La ribonucleoprotein 1B) This gene encodes a protein containing domains found in the La related protein of Drosophila melanogaster. La motif-containing proteins are thought to be RNA-binding proteins, where the La motif and adjacent amino acids fold into an RNA recognition motif. The La motif is also found in proteins unrelated to the La protein. Alternative splicing has been observed at this locus and multiple variants, encoding distinct isoforms, are described. Additional splice variation has been identified but the full-length nature of these transcripts has not been determined. [provided by RefSeq, Jun 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LARP1B	NM_018078.4	c.1524+16072A>G		intron_variant		ENST00000326639.11	NP_060548.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARP1B	ENST00000326639.11	c.1524+16072A>G		intron_variant		5	NM_018078.4	ENSP00000321997	A2

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89809 AN: 151816 Hom.: 27701 Cov.: 31

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.650

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.591 AC: 89866 AN: 151934 Hom.: 27714 Cov.: 31 AF XY: 0.593 AC XY: 44051 AN XY: 74254

Gnomad4 AFR AF: 0.419

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.491

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.654

Alfa AF: 0.602 Hom.: 4159

Bravo AF: 0.589

Asia WGS AF: 0.606 AC: 2084 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870687; hg19: chr4-129059415;