12-50437111-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_052879.5(LARP4):​c.536-624T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,112 control chromosomes in the GnomAD database, including 54,505 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 0.82 (54505 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

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>C		intron	N/A	NP_443111.4
	LARP4	NM_001330415.2		c.554-624T>C		intron	N/A	NP_001317344.1	Q71RC2-4
	LARP4	NM_001352305.2		c.551-624T>C		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>C		intron	N/A	ENSP00000381490.2	Q71RC2-1
	LARP4	ENST00000518444.5	TSL:1	c.533-624T>C		intron	N/A	ENSP00000429077.1	Q71RC2-3
	LARP4	ENST00000293618.12	TSL:1	c.536-624T>C		intron	N/A	ENSP00000293618.8	Q71RC2-6

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124994 AN: 151994 Hom.: 54477 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.844

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

GnomAD4 genome AF: 0.822 AC: 125062 AN: 152112 Hom.: 54505 Cov.: 31 AF XY: 0.828 AC XY: 61559 AN XY: 74352

African (AFR) AF: 0.500 AC: 20711 AN: 41426

American (AMR) AF: 0.893 AC: 13641 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3142 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5058 AN: 5180

South Asian (SAS) AF: 0.883 AC: 4252 AN: 4818

European-Finnish (FIN) AF: 0.983 AC: 10431 AN: 10608

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.954 AC: 64910 AN: 68020

Other (OTH) AF: 0.846 AC: 1787 AN: 2112

Alfa AF: 0.832 Hom.: 4248

Bravo AF: 0.802

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.42
DANN	Benign	0.42
PhyloP100		-1.4
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: rs4424740; hg19: chr12-50830894;