chr10-827087-A-G

Variant names:

• chr10-827087-A-G
• rs2839949
• NM_015155.3:c.1126-1217T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015155.3. 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
	LARP4B	NM_015155.3	MANE Select	c.1126-1217T>C		intron	N/A	NP_055970.1	Q92615
	LARP4B	NM_001351277.2		c.1126-1217T>C		intron	N/A	NP_001338206.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP4B	ENST00000316157.8	TSL:1 MANE Select	c.1126-1217T>C		intron	N/A	ENSP00000326128.3	Q92615
	LARP4B	ENST00000689323.1		c.4117-1217T>C		intron	N/A	ENSP00000510165.1	A0A8I5KVU2
	LARP4B	ENST00000912775.1		c.1126-1217T>C		intron	N/A	ENSP00000582834.1

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

African (AFR) AF: 0.513 AC: 21269 AN: 41420

American (AMR) AF: 0.404 AC: 6163 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3472

East Asian (EAS) AF: 0.421 AC: 2174 AN: 5168

South Asian (SAS) AF: 0.635 AC: 3057 AN: 4812

European-Finnish (FIN) AF: 0.573 AC: 6049 AN: 10548

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32112 AN: 67952

Other (OTH) AF: 0.472 AC: 995 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		-0.20
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: rs2839949; hg19: chr10-873027;