rs10904587

Variant names:

• chr10-941673-G-T
• rs10904587
• ENST00000435531.1:n.91-514G>T

Variant summary

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

The ENST00000435531.1(LARP4B-DT):​n.91-514G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 152,136 control chromosomes in the GnomAD database, including 11,999 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 0.39 (11999 hom., cov: 34)
• Consequence: LARP4B-DT ENST00000435531.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561
• Publications: 1 publications found

Genes affected

LARP4B-DT (HGNC:55786): (LARP4B divergent transcript)

ENSG00000205740 (HGNC:):

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LARP4B-DT	NR_120629.1	n.91-514G>T		intron_variant	Intron 1 of 2
LARP4B	XM_047424893.1	c.-196-6656C>A		intron_variant	Intron 2 of 19		XP_047280849.1
LARP4B	XM_047424894.1	c.-196-6656C>A		intron_variant	Intron 2 of 19		XP_047280850.1
LARP4B	XM_047424897.1	c.-196-6656C>A		intron_variant	Intron 2 of 19		XP_047280853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LARP4B-DT	ENST00000435531.1	n.91-514G>T		intron_variant	Intron 1 of 2	3
ENSG00000205740	ENST00000777599.1	n.343-6656C>A		intron_variant	Intron 2 of 2
LARP4B-DT	ENST00000777681.1	n.126-5633G>T		intron_variant	Intron 1 of 1
LARP4B-DT	ENST00000777682.1	n.147-514G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59031 AN: 152018 Hom.: 11971 Cov.: 34

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.389 AC: 59118 AN: 152136 Hom.: 11999 Cov.: 34 AF XY: 0.382 AC XY: 28411 AN XY: 74370

African (AFR) AF: 0.439 AC: 18212 AN: 41494

American (AMR) AF: 0.333 AC: 5087 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1163 AN: 3466

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5184

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4375 AN: 10594

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27486 AN: 67974

Other (OTH) AF: 0.391 AC: 827 AN: 2114

Alfa AF: 0.389 Hom.: 8652

Bravo AF: 0.382

Asia WGS AF: 0.188 AC: 657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10904587; hg19: chr10-987613;