10-46063201-C-T

Variant names:

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

Variant summary

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

The ENST00000623642.2(RPL23AP61):​n.-49C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 597,930 control chromosomes in the GnomAD database, including 81,051 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 0.46 (17631 hom., cov: 31)
  • Exomes 𝑓: 0.53 (63420 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 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.-49C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70252 AN: 151814 Hom.: 17640 Cov.: 31

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.466

GnomAD4 exome AF: 0.527 AC: 234964 AN: 445998 Hom.: 63420 Cov.: 0 AF XY: 0.519 AC XY: 126641 AN XY: 243914

African (AFR) AF: 0.252 AC: 3086 AN: 12252

American (AMR) AF: 0.618 AC: 15541 AN: 25164

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 5516 AN: 12166

East Asian (EAS) AF: 0.536 AC: 15590 AN: 29076

South Asian (SAS) AF: 0.418 AC: 21672 AN: 51834

European-Finnish (FIN) AF: 0.624 AC: 16182 AN: 25950

Middle Eastern (MID) AF: 0.384 AC: 1160 AN: 3024

European-Non Finnish (NFE) AF: 0.549 AC: 144240 AN: 262830

Other (OTH) AF: 0.505 AC: 11977 AN: 23702

GnomAD4 genome AF: 0.462 AC: 70250 AN: 151932 Hom.: 17631 Cov.: 31 AF XY: 0.464 AC XY: 34454 AN XY: 74268

African (AFR) AF: 0.255 AC: 10542 AN: 41408

American (AMR) AF: 0.541 AC: 8257 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2701 AN: 5166

South Asian (SAS) AF: 0.413 AC: 1990 AN: 4818

European-Finnish (FIN) AF: 0.611 AC: 6432 AN: 10528

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37244 AN: 67962

Other (OTH) AF: 0.461 AC: 972 AN: 2108

Alfa AF: 0.521 Hom.: 55930

Bravo AF: 0.453

Asia WGS AF: 0.414 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	12
DANN	Benign	0.87
PhyloP100		0.035

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7920517;

hg19: chr10-51532621;