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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484315.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL36AP2	ENST00000484315.1	TSL:6	n.138T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000258760	ENST00000553754.1	TSL:4	n.368+479A>G		intron	N/A
	ENSG00000258760	ENST00000555736.1	TSL:5	n.153-21243A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1256517;

hg19: chr14-65735684;

COSMIC: COSV72078052;