chr11-61632017-G-C

Variant names:

• chr11-61632017-G-C
• rs1692126
• ENST00000475331.1:n.332+1729G>C

Variant summary

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

The ENST00000475331.1(RPLP0P2):​n.332+1729G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,908 control chromosomes in the GnomAD database, including 10,673 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 (10673 hom., cov: 31)
• Consequence: RPLP0P2 ENST00000475331.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 3 publications found

Genes affected

RPLP0P2 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000475331.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPLP0P2	NR_002775.2		n.434+2978G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPLP0P2	ENST00000475331.1	TSL:4	n.332+1729G>C		intron	N/A
	RPLP0P2	ENST00000475561.5	TSL:4	n.387+1729G>C		intron	N/A
	RPLP0P2	ENST00000478959.1	TSL:4	n.433+2978G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54786 AN: 151790 Hom.: 10636 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.361 AC: 54858 AN: 151908 Hom.: 10673 Cov.: 31 AF XY: 0.353 AC XY: 26201 AN XY: 74250

African (AFR) AF: 0.488 AC: 20201 AN: 41432

American (AMR) AF: 0.273 AC: 4169 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1554 AN: 3464

East Asian (EAS) AF: 0.0647 AC: 335 AN: 5174

South Asian (SAS) AF: 0.229 AC: 1106 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2817 AN: 10536

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23505 AN: 67930

Other (OTH) AF: 0.351 AC: 737 AN: 2102

Alfa AF: 0.189 Hom.: 353

Bravo AF: 0.369

Asia WGS AF: 0.171 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.42
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1692126; hg19: chr11-61399489;