5-159279971-C-G

Variant names:

• chr5-159279971-C-G
• rs1368437
• NM_145049.5:c.801+1617C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145049.5(UBLCP1):​c.801+1617C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 151,868 control chromosomes in the GnomAD database, including 853 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 0.10 (853 hom., cov: 32)
• Consequence: UBLCP1 NM_145049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBLCP1	NM_145049.5	c.801+1617C>G		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.801+1617C>G		intron_variant	Intron 9 of 10	1	NM_145049.5	ENSP00000296786.6
UBLCP1	ENST00000519276.1	n.297+1617C>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15749 AN: 151756 Hom.: 847 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.0590

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.0716

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.104 AC: 15769 AN: 151868 Hom.: 853 Cov.: 32 AF XY: 0.101 AC XY: 7462 AN XY: 74206

African (AFR) AF: 0.106 AC: 4401 AN: 41462

American (AMR) AF: 0.115 AC: 1755 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3466

East Asian (EAS) AF: 0.0592 AC: 307 AN: 5188

South Asian (SAS) AF: 0.0641 AC: 308 AN: 4806

European-Finnish (FIN) AF: 0.0716 AC: 748 AN: 10442

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7226 AN: 67918

Other (OTH) AF: 0.116 AC: 244 AN: 2108

Alfa AF: 0.0421 Hom.: 39

Bravo AF: 0.110

Asia WGS AF: 0.0690 AC: 239 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.5
DANN	Benign	0.70
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

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: rs1368437; hg19: chr5-158706979;