ENST00000623642.2:n.-49C>G

Variant names:

• chr10-46063201-C-G
• rs7920517
• ENST00000623642.2:n.-49C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000623642.2(RPL23AP61):​n.-49C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RPL23AP61 ENST00000623642.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 40 publications found

Genes affected

RPL23AP61 (HGNC:36016): (ribosomal protein L23a pseudogene 61)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL23AP61	ENST00000623642.2	n.-49C>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 446928 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 244458

African (AFR) AF: 0.00 AC: 0 AN: 12276

American (AMR) AF: 0.00 AC: 0 AN: 25208

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12194

East Asian (EAS) AF: 0.00 AC: 0 AN: 29136

South Asian (SAS) AF: 0.00 AC: 0 AN: 51938

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26012

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3030

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 263384

Other (OTH) AF: 0.00 AC: 0 AN: 23750

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 55930

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.3
DANN	Benign	0.72
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs7920517; hg19: chr10-51532621;