rs4424740

Variant names:

• chr12-50437111-T-A
• rs4424740
• NM_052879.5:c.536-624T>A

Your query was ambiguous. Multiple possible variants found:

• chr12-50437111-T-A
• chr12-50437111-T-C
• chr12-50437111-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_052879.5(LARP4):​c.536-624T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LARP4 NM_052879.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 1 publications found

Genes affected

LARP4 (HGNC:24320): (La ribonucleoprotein 4) Enables mRNA 3'-UTR binding activity and poly(A) binding activity. Involved in cytoskeleton organization; positive regulation of translation; and regulation of cell morphogenesis. Located in cytosol. Colocalizes with cytoplasmic stress granule; cytosolic small ribosomal subunit; and polysome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052879.5. 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
	LARP4	NM_052879.5	MANE Select	c.536-624T>A		intron	N/A	NP_443111.4
	LARP4	NM_001330415.2		c.554-624T>A		intron	N/A	NP_001317344.1	Q71RC2-4
	LARP4	NM_001352305.2		c.551-624T>A		intron	N/A	NP_001339234.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LARP4	ENST00000398473.7	TSL:1 MANE Select	c.536-624T>A		intron	N/A	ENSP00000381490.2	Q71RC2-1
	LARP4	ENST00000518444.5	TSL:1	c.533-624T>A		intron	N/A	ENSP00000429077.1	Q71RC2-3
	LARP4	ENST00000293618.12	TSL:1	c.536-624T>A		intron	N/A	ENSP00000293618.8	Q71RC2-6

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 4248

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.37
PhyloP100		-1.4

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: rs4424740; hg19: chr12-50830894;