10-46063455-T-C

Position:

• chr10-46063455-T-C

Variant summary

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

The ENST00000623642.2(RPL23AP61):​n.206T>C 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 0.553 in 790,272 control chromosomes in the GnomAD database, including 122,562 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 0.57 (24709 hom., cov: 31)
  • Exomes 𝑓: 0.55 (97853 hom.)
• Consequence: RPL23AP61 ENST00000623642.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.61

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=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 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
RPL23AP61	ENST00000623642.2	n.206T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86290 AN: 151828 Hom.: 24685 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.548

GnomAD4 exome AF: 0.549 AC: 350624 AN: 638324 Hom.: 97853 Cov.: 7 AF XY: 0.540 AC XY: 187649 AN XY: 347364

Gnomad4 AFR exome AF: 0.596

Gnomad4 AMR exome AF: 0.653

Gnomad4 ASJ exome AF: 0.453

Gnomad4 EAS exome AF: 0.542

Gnomad4 SAS exome AF: 0.434

Gnomad4 FIN exome AF: 0.619

Gnomad4 NFE exome AF: 0.558

Gnomad4 OTH exome AF: 0.536

GnomAD4 genome AF: 0.568 AC: 86359 AN: 151948 Hom.: 24709 Cov.: 31 AF XY: 0.566 AC XY: 42037 AN XY: 74294

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.544

Alfa AF: 0.571 Hom.: 2954

Bravo AF: 0.575

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	5.3
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4581397; hg19: chr10-51532367;