10-46063455-T-C

Variant names:

• chr10-46063455-T-C
• rs4581397
• ENST00000623642.2:n.206T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623642.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL23AP61	ENST00000623642.2	TSL:6	n.206T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.596 AC: 10722 AN: 17976

American (AMR) AF: 0.653 AC: 28555 AN: 43698

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 9543 AN: 21086

East Asian (EAS) AF: 0.542 AC: 19568 AN: 36136

South Asian (SAS) AF: 0.434 AC: 30421 AN: 70164

European-Finnish (FIN) AF: 0.619 AC: 24237 AN: 39126

Middle Eastern (MID) AF: 0.413 AC: 1182 AN: 2862

European-Non Finnish (NFE) AF: 0.558 AC: 208410 AN: 373718

Other (OTH) AF: 0.536 AC: 17986 AN: 33558

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

African (AFR) AF: 0.598 AC: 24751 AN: 41418

American (AMR) AF: 0.595 AC: 9093 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1574 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2789 AN: 5148

South Asian (SAS) AF: 0.430 AC: 2068 AN: 4808

European-Finnish (FIN) AF: 0.614 AC: 6479 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37887 AN: 67970

Other (OTH) AF: 0.544 AC: 1148 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	5.3
DANN	Benign	0.92
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs4581397; hg19: chr10-51532367;