10-46063294-C-T

Variant names:

• chr10-46063294-C-T
• rs4630240
• ENST00000623642.2:n.45C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.403 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.45C>T		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.0733 AC: 1190 AN: 16244

American (AMR) AF: 0.497 AC: 18467 AN: 37134

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 5898 AN: 19336

East Asian (EAS) AF: 0.390 AC: 13921 AN: 35718

South Asian (SAS) AF: 0.287 AC: 18958 AN: 66064

European-Finnish (FIN) AF: 0.426 AC: 15970 AN: 37506

Middle Eastern (MID) AF: 0.266 AC: 1053 AN: 3958

European-Non Finnish (NFE) AF: 0.404 AC: 138160 AN: 341942

Other (OTH) AF: 0.351 AC: 11044 AN: 31468

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

African (AFR) AF: 0.0776 AC: 3220 AN: 41506

American (AMR) AF: 0.412 AC: 6285 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1063 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2058 AN: 5152

South Asian (SAS) AF: 0.278 AC: 1334 AN: 4806

European-Finnish (FIN) AF: 0.424 AC: 4473 AN: 10546

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27394 AN: 67944

Other (OTH) AF: 0.308 AC: 652 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	3.9
DANN	Benign	0.96
PhyloP100		-1.3

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: rs4630240;

hg19: chr10-51532528;