10-832955-G-A

Variant names:

• chr10-832955-G-A
• rs11817793
• NM_015155.3:c.751-1978C>T

Variant summary

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

The NM_015155.3(LARP4B):​c.751-1978C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,012 control chromosomes in the GnomAD database, including 2,136 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 0.16 (2136 hom., cov: 32)
• Consequence: LARP4B NM_015155.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LARP4B	NM_015155.3	c.751-1978C>T		intron_variant	Intron 8 of 17	ENST00000316157.8	NP_055970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LARP4B	ENST00000316157.8	c.751-1978C>T		intron_variant	Intron 8 of 17	1	NM_015155.3	ENSP00000326128.3
LARP4B	ENST00000689323.1	c.3742-1978C>T		intron_variant	Intron 6 of 15			ENSP00000510165.1
LARP4B	ENST00000688365.1	c.604-1978C>T		intron_variant	Intron 5 of 15			ENSP00000509705.1
LARP4B	ENST00000690516.1	n.*123-1978C>T		intron_variant	Intron 7 of 16			ENSP00000508832.1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24498 AN: 151894 Hom.: 2121 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.0739

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.0703

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.162 AC: 24555 AN: 152012 Hom.: 2136 Cov.: 32 AF XY: 0.158 AC XY: 11707 AN XY: 74286

African (AFR) AF: 0.154 AC: 6379 AN: 41476

American (AMR) AF: 0.168 AC: 2574 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0739 AC: 256 AN: 3466

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5184

South Asian (SAS) AF: 0.0697 AC: 336 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1806 AN: 10528

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12716 AN: 67948

Other (OTH) AF: 0.161 AC: 339 AN: 2102

Alfa AF: 0.167 Hom.: 371

Bravo AF: 0.161

Asia WGS AF: 0.0540 AC: 188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.24
DANN	Benign	0.53
PhyloP100		-0.29
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: rs11817793; hg19: chr10-878895;