2-152877408-T-C

Variant names:

• chr2-152877408-T-C
• rs1427395
• ENST00000446233.1:n.589T>C

Variant summary

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

The ENST00000446233.1(UBQLN4P2):​n.589T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBQLN4P2 ENST00000446233.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 2 publications found

Genes affected

UBQLN4P2 (HGNC:38662): (ubiquilin 4 pseudogene 2)

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=-0.61).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBQLN4P2		n.152877408T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBQLN4P2	ENST00000446233.1	n.589T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 23778 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 13530

African (AFR) AF: 0.00 AC: 0 AN: 570

American (AMR) AF: 0.00 AC: 0 AN: 2156

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 396

East Asian (EAS) AF: 0.00 AC: 0 AN: 940

South Asian (SAS) AF: 0.00 AC: 0 AN: 2152

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1388

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 64

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 14886

Other (OTH) AF: 0.00 AC: 0 AN: 1226

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 893

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1427395; hg19: chr2-153733922;