rs1256517

Positions:

• chr14-65268966-T-C

Variant summary

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

The ENST00000484315.1(RPL36AP2):​n.138T>C 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 0.199 in 223,070 control chromosomes in the GnomAD database, including 7,183 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 0.23 (6302 hom., cov: 32)
  • Exomes 𝑓: 0.14 (881 hom.)
• Consequence: RPL36AP2 ENST00000484315.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.21

Genes affected

RPL36AP2 (HGNC:19777): (ribosomal protein L36a pseudogene 2)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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
RPL36AP2	ENST00000484315.1	n.138T>C		non_coding_transcript_exon_variant	1/1
	ENST00000555736.1	n.153-21243A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000553754.1	n.368+479A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34552 AN: 151992 Hom.: 6276 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0907

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.231

GnomAD4 exome AF: 0.139 AC: 9841 AN: 70960 Hom.: 881 Cov.: 0 AF XY: 0.137 AC XY: 5816 AN XY: 42440

Gnomad4 AFR exome AF: 0.530

Gnomad4 AMR exome AF: 0.102

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.288

Gnomad4 SAS exome AF: 0.134

Gnomad4 FIN exome AF: 0.110

Gnomad4 NFE exome AF: 0.118

Gnomad4 OTH exome AF: 0.118

GnomAD4 genome AF: 0.228 AC: 34622 AN: 152110 Hom.: 6302 Cov.: 32 AF XY: 0.224 AC XY: 16673 AN XY: 74364

Gnomad4 AFR AF: 0.499

Gnomad4 AMR AF: 0.166

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0907

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.236

Alfa AF: 0.136 Hom.: 1107

Bravo AF: 0.246

Asia WGS AF: 0.238 AC: 828 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.6
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1256517; hg19: chr14-65735684; COSMIC: COSV72078052;