rs4834232

chr4-128103118-C-T

Variant summary

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

The NM_018078.4(LARP1B):c.814-4021C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,076 control chromosomes in the GnomAD database, including 2,889 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 0.18 (2889 hom., cov: 32)
• Consequence: LARP1B NM_018078.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.505

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=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LARP1B	NM_018078.4	c.814-4021C>T		intron_variant		ENST00000326639.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LARP1B	ENST00000326639.11	c.814-4021C>T		intron_variant		5	NM_018078.4	A2

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26890 AN: 151958 Hom.: 2887 Cov.: 32

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.177 AC: 26910 AN: 152076 Hom.: 2889 Cov.: 32 AF XY: 0.179 AC XY: 13313 AN XY: 74342

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.213

Alfa AF: 0.220 Hom.: 8049

Bravo AF: 0.172

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.24
Dann	Benign	0.56

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: rs4834232; hg19: chr4-129024273;