11-61622896-C-T

Position:

• chr11-61622896-C-T

Variant summary

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

The NR_002775.2(RPLP0P2):​n.94-2089C>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 0.153 in 152,200 control chromosomes in the GnomAD database, including 2,352 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 0.15 (2352 hom., cov: 32)
• Consequence: RPLP0P2 NR_002775.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.857

Genes affected

RPLP0P2 (HGNC:17960): (ribosomal protein lateral stalk subunit P0 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPLP0P2	NR_002775.2	n.94-2089C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPLP0P2	ENST00000496593.5	n.94-2089C>T		intron_variant, non_coding_transcript_variant		2
RPLP0P2	ENST00000478959.1	n.93-2089C>T		intron_variant, non_coding_transcript_variant		4
RPLP0P2	ENST00000702537.1	n.180+486C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23344 AN: 152082 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.0380

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0526

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23357 AN: 152200 Hom.: 2352 Cov.: 32 AF XY: 0.159 AC XY: 11823 AN XY: 74428

Gnomad4 AFR AF: 0.0379

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.245

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.158

Alfa AF: 0.180 Hom.: 1481

Bravo AF: 0.149

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.36
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1495941; hg19: chr11-61390368;