10-97414113-T-C

Variant names:

• chr10-97414113-T-C
• rs11189211
• ENST00000536831.6:c.-138+11910A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

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]

ENSG00000231970 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439965.6. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RRP12	ENST00000536831.6	TSL:5	c.-138+11910A>G		intron	N/A	ENSP00000446184.2	Q5JTH9-1
	RRP12	ENST00000439965.6	TSL:4	c.-138+10686A>G		intron	N/A	ENSP00000401102.3	H7C1M8
	RRP12	ENST00000622320.4	TSL:4	c.-393-4254A>G		intron	N/A	ENSP00000482139.1	A0A087WYW2

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

African (AFR) AF: 0.512 AC: 21206 AN: 41440

American (AMR) AF: 0.328 AC: 5003 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3468

East Asian (EAS) AF: 0.510 AC: 2634 AN: 5168

South Asian (SAS) AF: 0.397 AC: 1914 AN: 4824

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10564

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17918 AN: 67938

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.301 Hom.: 30059

Bravo AF: 0.364

Asia WGS AF: 0.469 AC: 1629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.65
PhyloP100		0.029

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11189211;

hg19: chr10-99173870;