rs2675705

chr10-86631504-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000481963.1(RPL7AP8):n.125G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.291 in 921,162 control chromosomes in the GnomAD database, including 41,292 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 0.30 (6874 hom., cov: 32)
  • Exomes 𝑓: 0.29 (34418 hom.)
• Consequence: RPL7AP8 ENST00000481963.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.72

Genes affected

RPL7AP8 (HGNC:23738): (ribosomal protein L7a pseudogene 8)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL7AP8	ENST00000481963.1	n.125G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45065 AN: 151888 Hom.: 6864 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.301

GnomAD4 exome AF: 0.290 AC: 222791 AN: 769156 Hom.: 34418 Cov.: 10 AF XY: 0.286 AC XY: 116891 AN XY: 408058

Gnomad4 AFR exome AF: 0.278

Gnomad4 AMR exome AF: 0.373

Gnomad4 ASJ exome AF: 0.287

Gnomad4 EAS exome AF: 0.523

Gnomad4 SAS exome AF: 0.253

Gnomad4 FIN exome AF: 0.290

Gnomad4 NFE exome AF: 0.271

Gnomad4 OTH exome AF: 0.299

GnomAD4 genome AF: 0.297 AC: 45094 AN: 152006 Hom.: 6874 Cov.: 32 AF XY: 0.300 AC XY: 22297 AN XY: 74280

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.298

Alfa AF: 0.280 Hom.: 729

Bravo AF: 0.306

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
Cadd	Benign	2.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2675705; hg19: chr10-88391261;