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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL23AP61		n.46063294C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL23AP61	ENST00000623642.2	n.45C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs4630240; hg19: chr10-51532528;