10-46063294-C-T

Position:

• chr10-46063294-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000623642.2(RPL23AP61):​n.45C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 741,380 control chromosomes in the GnomAD database, including 54,117 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 0.31 (8916 hom., cov: 32)
  • Exomes 𝑓: 0.38 (45201 hom.)
• Consequence: RPL23AP61 ENST00000623642.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL23AP61	ENST00000623642.2	n.45C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46971 AN: 151892 Hom.: 8914 Cov.: 32

Gnomad AFR AF: 0.0779

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.312

GnomAD4 exome AF: 0.381 AC: 224661 AN: 589370 Hom.: 45201 Cov.: 3 AF XY: 0.376 AC XY: 121345 AN XY: 322782

Gnomad4 AFR exome AF: 0.0733

Gnomad4 AMR exome AF: 0.497

Gnomad4 ASJ exome AF: 0.305

Gnomad4 EAS exome AF: 0.390

Gnomad4 SAS exome AF: 0.287

Gnomad4 FIN exome AF: 0.426

Gnomad4 NFE exome AF: 0.404

Gnomad4 OTH exome AF: 0.351

GnomAD4 genome AF: 0.309 AC: 46966 AN: 152010 Hom.: 8916 Cov.: 32 AF XY: 0.310 AC XY: 22991 AN XY: 74244

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.308

Alfa AF: 0.360 Hom.: 1373

Bravo AF: 0.305

Asia WGS AF: 0.286 AC: 999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	3.9
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4630240; hg19: chr10-51532528;