rs7895695

Positions:

• chr10-97407498-G-A
• chr10-97407498-G-T

Variant summary

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

The ENST00000422848.1(ENSG00000231970):​n.259+6125G>A 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 0.337 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: ENST00000422848.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.88

Genes affected

(HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000422848.1	n.259+6125G>A		intron_variant, non_coding_transcript_variant		3
RRP12	ENST00000439965.6	c.-137-6130C>T		intron_variant		4		ENSP00000401102
RRP12	ENST00000536831.5	c.-137-6130C>T		intron_variant		5		ENSP00000446184	P1
RRP12	ENST00000622320.4	c.-138+2026C>T		intron_variant		4		ENSP00000482139

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

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.327

Alfa AF: 0.288 Hom.: 10764

Bravo AF: 0.338

Asia WGS AF: 0.356 AC: 1239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs7895695; hg19: chr10-99167255;