rs1368438

Variant names:

• chr5-159280297-C-T
• rs1368438
• NM_145049.5:c.801+1943C>T

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+1943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,088 control chromosomes in the GnomAD database, including 15,618 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 0.44 (15618 hom., cov: 32)
• Consequence: UBLCP1 NM_145049.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBLCP1	NM_145049.5	c.801+1943C>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.801+1943C>T		intron_variant	Intron 9 of 10	1	NM_145049.5	ENSP00000296786.6
UBLCP1	ENST00000519276.1	n.297+1943C>T		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66754 AN: 151972 Hom.: 15619 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.439 AC: 66775 AN: 152088 Hom.: 15618 Cov.: 32 AF XY: 0.445 AC XY: 33058 AN XY: 74328

African (AFR) AF: 0.281 AC: 11675 AN: 41476

American (AMR) AF: 0.419 AC: 6407 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.487 AC: 1688 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2479 AN: 5170

South Asian (SAS) AF: 0.441 AC: 2125 AN: 4818

European-Finnish (FIN) AF: 0.608 AC: 6431 AN: 10570

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34481 AN: 67984

Other (OTH) AF: 0.424 AC: 895 AN: 2112

Alfa AF: 0.477 Hom.: 9777

Bravo AF: 0.416

Asia WGS AF: 0.428 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.39
PhyloP100		-0.53
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: rs1368438; hg19: chr5-158707305;