10-827087-A-G

Position:

• chr10-827087-A-G

Variant summary

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

The NM_015155.3(LARP4B):​c.1126-1217T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 151,960 control chromosomes in the GnomAD database, including 18,233 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 0.49 (18233 hom., cov: 31)
• Consequence: LARP4B NM_015155.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203

Genes affected

LARP4B (HGNC:28987): (La ribonucleoprotein 4B) This gene encodes a member of an evolutionarily conserved protein family implicated in RNA metabolism and translation. Members of this family are characterized by the presence of an La motif, which is often located adjacent to one or more RNA recognition motifs (RRM). Together, the two motifs constitute the functional region of the protein and enable its interaction with the RNA substrate. This protein family is divided into five sub-families: the genuine La proteins and four La-related protein (LARP) sub-families. The protein encoded by this gene belongs to LARP sub-family 4. It is a cytoplasmic protein that may play a stimulatory role in translation. [provided by RefSeq, Oct 2012]

LARP4B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LARP4B	NM_015155.3	c.1126-1217T>C		intron_variant		ENST00000316157.8	NP_055970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARP4B	ENST00000316157.8	c.1126-1217T>C		intron_variant		1	NM_015155.3	ENSP00000326128.3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73903 AN: 151842 Hom.: 18200 Cov.: 31

Gnomad AFR AF: 0.513

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.487 AC: 73986 AN: 151960 Hom.: 18233 Cov.: 31 AF XY: 0.492 AC XY: 36564 AN XY: 74282

Gnomad4 AFR AF: 0.513

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.472

Alfa AF: 0.488 Hom.: 2216

Bravo AF: 0.467

Asia WGS AF: 0.544 AC: 1892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.46

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: rs2839949; hg19: chr10-873027;