10-95595157-C-T

Variant summary

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

The ENST00000398190.2(RPS3AP36):n.560C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.466 in 759,106 control chromosomes in the GnomAD database, including 88,666 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 0.39 (14440 hom., cov: 33)
  • Exomes 𝑓: 0.48 (74226 hom.)
• Consequence: RPS3AP36 ENST00000398190.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.65

Genes affected

RPS3AP36 (HGNC:35596): (RPS3A pseudogene 36)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 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
RPS3AP36	ENST00000398190.2	n.560C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59954 AN: 152018 Hom.: 14441 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.484 AC: 293583 AN: 606970 Hom.: 74226 Cov.: 4 AF XY: 0.476 AC XY: 157761 AN XY: 331606

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.570

Gnomad4 ASJ exome AF: 0.350

Gnomad4 EAS exome AF: 0.511

Gnomad4 SAS exome AF: 0.373

Gnomad4 FIN exome AF: 0.531

Gnomad4 NFE exome AF: 0.518

Gnomad4 OTH exome AF: 0.459

GnomAD4 genome AF: 0.394 AC: 59953 AN: 152136 Hom.: 14440 Cov.: 33 AF XY: 0.393 AC XY: 29239 AN XY: 74362

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.366

Alfa AF: 0.446 Hom.: 2101

Bravo AF: 0.386

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	6.7
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs498055; hg19: chr10-97354914;