rs1368438

Positions:

• chr5-159280297-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+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

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=-0.98).
• 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/exons	MANE	UniProt
UBLCP1	NM_145049.5	c.801+1943C>T		intron_variant		ENST00000296786.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBLCP1	ENST00000296786.8	c.801+1943C>T		intron_variant		1	NM_145049.5	P1
UBLCP1	ENST00000519276.1	n.297+1943C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.608

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.424

Alfa AF: 0.478 Hom.: 8800

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

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: rs1368438; hg19: chr5-158707305;