chr10-97414113-T-C

Position:

• chr10-97414113-T-C

Variant summary

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

The ENST00000439965.6(RRP12):​c.-138+10686A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 151,988 control chromosomes in the GnomAD database, including 10,614 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 0.36 (10614 hom., cov: 32)
• Consequence: RRP12 ENST00000439965.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

Genes affected

RRP12 (HGNC:29100): (ribosomal RNA processing 12 homolog) Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in cytosol; nucleolus; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.97414113T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RRP12	ENST00000536831.5	c.-138+11910A>G		intron_variant		5		ENSP00000446184.2
RRP12	ENST00000439965.6	c.-138+10686A>G		intron_variant		4		ENSP00000401102.3
RRP12	ENST00000622320.4	c.-393-4254A>G		intron_variant		4		ENSP00000482139.1
ENSG00000231970	ENST00000422848.1	n.260-5123T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54264 AN: 151870 Hom.: 10600 Cov.: 32

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.357 AC: 54307 AN: 151988 Hom.: 10614 Cov.: 32 AF XY: 0.359 AC XY: 26682 AN XY: 74316

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.327

Alfa AF: 0.289 Hom.: 12899

Bravo AF: 0.364

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.65

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

Publications

LitVar

Other links and lift over

dbSNP: rs11189211; hg19: chr10-99173870;