chr5-159282974-A-T

Variant names:

• chr5-159282974-A-T
• rs10515783
• NM_145049.5:c.802-238A>T

Variant summary

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

The NM_145049.5(UBLCP1):​c.802-238A>T 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 151,944 control chromosomes in the GnomAD database, including 6,195 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 (6195 hom., cov: 32)
• Consequence: UBLCP1 NM_145049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

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=-0.77).
• 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 rank	MANE	Protein	UniProt
UBLCP1	NM_145049.5	c.802-238A>T		intron_variant	Intron 9 of 10	ENST00000296786.8	NP_659486.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBLCP1	ENST00000296786.8	c.802-238A>T		intron_variant	Intron 9 of 10	1	NM_145049.5	ENSP00000296786.6
UBLCP1	ENST00000519276.1	n.298-238A>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41709 AN: 151826 Hom.: 6198 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.275 AC: 41709 AN: 151944 Hom.: 6195 Cov.: 32 AF XY: 0.278 AC XY: 20642 AN XY: 74238

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.243

Alfa AF: 0.295 Hom.: 838

Bravo AF: 0.260

Asia WGS AF: 0.279 AC: 974 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	13
DANN	Benign	0.87

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: rs10515783; hg19: chr5-158709982;