4-128138260-A-G

Variant names:

• chr4-128138260-A-G
• rs1870687
• NM_018078.4:c.1524+16072A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018078.4. 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
	LARP1B	NM_018078.4	MANE Select	c.1524+16072A>G		intron	N/A	NP_060548.2
	LARP1B	NM_001410786.1		c.1524+16072A>G		intron	N/A	NP_001397715.1	A0A994J4X5
	LARP1B	NM_001350531.2		c.801+16072A>G		intron	N/A	NP_001337460.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP1B	ENST00000326639.11	TSL:5 MANE Select	c.1524+16072A>G		intron	N/A	ENSP00000321997.6	Q659C4-1
	LARP1B	ENST00000507259.5	TSL:1	n.72+16072A>G		intron	N/A	ENSP00000423686.1	H0Y9B4
	LARP1B	ENST00000899921.1		c.1524+16072A>G		intron	N/A	ENSP00000569980.1

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

African (AFR) AF: 0.419 AC: 17374 AN: 41416

American (AMR) AF: 0.698 AC: 10643 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2479 AN: 3472

East Asian (EAS) AF: 0.491 AC: 2539 AN: 5172

South Asian (SAS) AF: 0.733 AC: 3533 AN: 4822

European-Finnish (FIN) AF: 0.607 AC: 6401 AN: 10542

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44611 AN: 67942

Other (OTH) AF: 0.654 AC: 1379 AN: 2108

Alfa AF: 0.597 Hom.: 4237

Bravo AF: 0.589

Asia WGS AF: 0.606 AC: 2084 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		0.14
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1870687; hg19: chr4-129059415;