rs10904587

Positions:

• chr10-941673-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120629.1(LARP4B-DT):​n.91-514G>T variant causes a intron, non coding transcript 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 NR_120629.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

Genes affected

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

LARP4B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LARP4B-DT	NR_120629.1	n.91-514G>T		intron_variant, non_coding_transcript_variant
LARP4B	XM_047424893.1	c.-196-6656C>A		intron_variant			XP_047280849.1
LARP4B	XM_047424894.1	c.-196-6656C>A		intron_variant			XP_047280850.1
LARP4B	XM_047424897.1	c.-196-6656C>A		intron_variant			XP_047280853.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LARP4B-DT	ENST00000435531.1	n.91-514G>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.333

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.413

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.391

Alfa AF: 0.396 Hom.: 4500

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10904587; hg19: chr10-987613;