chr2-46257171-C-T

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446949.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL36AP14	ENST00000446949.1	TSL:6	n.7G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000294354	ENST00000723079.1		n.107-902C>T		intron	N/A

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 v4.9

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;