10-97407498-G-A

Variant names:

• chr10-97407498-G-A
• rs7895695
• ENST00000536831.6:c.-137-6130C>T

Variant summary

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

The ENST00000439965.6(RRP12):​c.-137-6130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,814 control chromosomes in the GnomAD database, including 8,986 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 0.34 (8986 hom., cov: 31)
• Consequence: RRP12 ENST00000439965.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88
• Publications: 15 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 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.-137-6130C>T		intron	N/A	ENSP00000446184.2	Q5JTH9-1
	RRP12	ENST00000439965.6	TSL:4	c.-137-6130C>T		intron	N/A	ENSP00000401102.3	H7C1M8
	RRP12	ENST00000622320.4	TSL:4	c.-138+2026C>T		intron	N/A	ENSP00000482139.1	A0A087WYW2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51152 AN: 151696 Hom.: 8977 Cov.: 31

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.337 AC: 51180 AN: 151814 Hom.: 8986 Cov.: 31 AF XY: 0.339 AC XY: 25140 AN XY: 74202

African (AFR) AF: 0.435 AC: 17967 AN: 41290

American (AMR) AF: 0.334 AC: 5093 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1212 AN: 3466

East Asian (EAS) AF: 0.298 AC: 1542 AN: 5180

South Asian (SAS) AF: 0.364 AC: 1754 AN: 4820

European-Finnish (FIN) AF: 0.321 AC: 3385 AN: 10556

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19106 AN: 67946

Other (OTH) AF: 0.327 AC: 689 AN: 2110

Alfa AF: 0.298 Hom.: 20215

Bravo AF: 0.338

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.64
PhyloP100		2.9

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: rs7895695;

hg19: chr10-99167255;