5-159279705-C-T

Position:

• chr5-159279705-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145049.5(UBLCP1):​c.801+1351C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,062 control chromosomes in the GnomAD database, including 2,012 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 0.15 (2012 hom., cov: 32)
• Consequence: UBLCP1 NM_145049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

Genes affected

UBLCP1 (HGNC:28110): (ubiquitin like domain containing CTD phosphatase 1) Enables protein serine/threonine phosphatase activity. Involved in protein dephosphorylation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBLCP1	NM_145049.5	c.801+1351C>T		intron_variant		ENST00000296786.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBLCP1	ENST00000296786.8	c.801+1351C>T		intron_variant		1	NM_145049.5	P1
UBLCP1	ENST00000519276.1	n.297+1351C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23173 AN: 151944 Hom.: 2008 Cov.: 32

Gnomad AFR AF: 0.0755

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.167

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.152 AC: 23182 AN: 152062 Hom.: 2012 Cov.: 32 AF XY: 0.155 AC XY: 11491 AN XY: 74306

Gnomad4 AFR AF: 0.0754

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.170

Alfa AF: 0.162 Hom.: 567

Bravo AF: 0.143

Asia WGS AF: 0.145 AC: 503 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.36

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13153734; hg19: chr5-158706713;