4-54221414-C-T

Variant names:

• chr4-54221414-C-T
• rs17084051
• ENST00000507166.5:c.1018-53511C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000507166.5(ENSG00000282278):​c.1018-53511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000026 in 384,372 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000026 (0 hom.)
• Consequence: ENSG00000282278 ENST00000507166.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.57
• Publications: 0 publications found

Genes affected

ENSG00000282278 (HGNC:):

RPL22P13 (HGNC:36352): (ribosomal protein L22 pseudogene 13)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL22P13		n.54221414C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282278	ENST00000507166.5	c.1018-53511C>T		intron_variant	Intron 12 of 23	2		ENSP00000423325.1
RPL22P13	ENST00000493291.1	n.289C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000260 AC: 1 AN: 384372 Hom.: 0 Cov.: 0 AF XY: 0.00000482 AC XY: 1 AN XY: 207290

African (AFR) AF: 0.00 AC: 0 AN: 10048

American (AMR) AF: 0.00 AC: 0 AN: 15478

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12538

East Asian (EAS) AF: 0.00 AC: 0 AN: 22482

South Asian (SAS) AF: 0.00 AC: 0 AN: 42186

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37408

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3232

European-Non Finnish (NFE) AF: 0.00000454 AC: 1 AN: 220178

Other (OTH) AF: 0.00 AC: 0 AN: 20822

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	3.2
DANN	Benign	0.53
PhyloP100		1.6

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17084051; hg19: chr4-55087581;