rs17034876

Variant names:

• chr2-46257171-C-T
• rs17034876
• ENST00000446949.1:n.7G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446949.1(RPL36AP14):​n.7G>A 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 0.676 in 152,142 control chromosomes in the GnomAD database, including 34,997 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 0.68 (34980 hom., cov: 32)
  • Exomes 𝑓: 0.66 (17 hom.)
• Consequence: RPL36AP14 ENST00000446949.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.52
• Publications: 13 publications found

Genes affected

RPL36AP14 (HGNC:36788): (ribosomal protein L36a pseudogene 14)

ENSG00000294354 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL36AP14		n.46257171C>T		intragenic_variant
LOC101926974	XR_940051.4	n.32-902C>T		intron_variant	Intron 1 of 2
LOC105374581	XR_940052.3	n.-239G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL36AP14	ENST00000446949.1	n.7G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000294354	ENST00000723079.1	n.107-902C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102682 AN: 151944 Hom.: 34963 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.659 AC: 54 AN: 82 Hom.: 17 Cov.: 0 AF XY: 0.682 AC XY: 45 AN XY: 66

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.600 AC: 6 AN: 10

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.638 AC: 37 AN: 58

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.676 AC: 102741 AN: 152060 Hom.: 34980 Cov.: 32 AF XY: 0.670 AC XY: 49809 AN XY: 74336

African (AFR) AF: 0.679 AC: 28131 AN: 41454

American (AMR) AF: 0.618 AC: 9451 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2503 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2620 AN: 5166

South Asian (SAS) AF: 0.544 AC: 2616 AN: 4810

European-Finnish (FIN) AF: 0.717 AC: 7579 AN: 10576

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47603 AN: 67980

Other (OTH) AF: 0.666 AC: 1403 AN: 2108

Alfa AF: 0.688 Hom.: 67045

Bravo AF: 0.667

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.66
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs17034876; hg19: chr2-46484310;