5-159281057-A-G

Position:

• chr5-159281057-A-G

Variant summary

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

The NM_145049.5(UBLCP1):​c.802-2155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,178 control chromosomes in the GnomAD database, including 6,201 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 0.27 (6201 hom., cov: 32)
• Consequence: UBLCP1 NM_145049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBLCP1	NM_145049.5	c.802-2155A>G		intron_variant		ENST00000296786.8	NP_659486.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBLCP1	ENST00000296786.8	c.802-2155A>G		intron_variant		1	NM_145049.5	ENSP00000296786	P1
UBLCP1	ENST00000519276.1	n.298-2155A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41777 AN: 152060 Hom.: 6204 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.275 AC: 41777 AN: 152178 Hom.: 6201 Cov.: 32 AF XY: 0.278 AC XY: 20687 AN XY: 74414

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.244

Alfa AF: 0.299 Hom.: 1157

Bravo AF: 0.260

Asia WGS AF: 0.281 AC: 979 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs6887080; hg19: chr5-158708065;