rs1256517

Variant names:

• chr14-65268966-T-C
• rs1256517
• ENST00000484315.1:n.138T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000258760 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
RPL36AP2		n.65268966T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL36AP2	ENST00000484315.1	n.138T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000258760	ENST00000553754.1	n.368+479A>G		intron_variant	Intron 2 of 2	4
ENSG00000258760	ENST00000555736.1	n.153-21243A>G		intron_variant	Intron 1 of 3	5
ENSG00000305690	ENST00000812438.1	n.105+7490T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.530 AC: 1017 AN: 1918

American (AMR) AF: 0.102 AC: 822 AN: 8036

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 133 AN: 980

East Asian (EAS) AF: 0.288 AC: 1192 AN: 4136

South Asian (SAS) AF: 0.134 AC: 1066 AN: 7952

European-Finnish (FIN) AF: 0.110 AC: 862 AN: 7820

Middle Eastern (MID) AF: 0.196 AC: 20 AN: 102

European-Non Finnish (NFE) AF: 0.118 AC: 4408 AN: 37288

Other (OTH) AF: 0.118 AC: 321 AN: 2728

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

African (AFR) AF: 0.499 AC: 20701 AN: 41454

American (AMR) AF: 0.166 AC: 2538 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1452 AN: 5180

South Asian (SAS) AF: 0.120 AC: 577 AN: 4816

European-Finnish (FIN) AF: 0.0907 AC: 961 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7284 AN: 67994

Other (OTH) AF: 0.236 AC: 499 AN: 2112

Alfa AF: 0.139 Hom.: 1314

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
PhyloP100		-3.2

Splicing

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

Other links and lift over

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