Genetic Variant UPK3BL1:p.Leu224Phe (chr7-102638727-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001114403.3(UPK3BL1):c.670C>T(p.Leu224Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 25)

Exomes 𝑓: 0.000011 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

UPK3BL1
NM_001114403.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.198

Variant links:

Genes affected

UPK3BL1 (HGNC:37278): (uroplakin 3B like 1) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

UPK3BL1 links:

ENSG00000267645 (HGNC:):

ENSG00000267645 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.15547988).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UPK3BL1	NM_001114403.3 link	c.670C>T	p.Leu224Phe	missense_variant	Exon 5 of 6	ENST00000340457.8	NP_001107875.1	B0FP48E5RIL1
POLR2J2-UPK3BL1	NR_173352.1 link	n.1022C>T		non_coding_transcript_exon_variant	Exon 8 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
UPK3BL1	ENST00000340457.8 link	c.670C>T	p.Leu224Phe	missense_variant	Exon 5 of 6	1	NM_001114403.3	ENSP00000342938.8	B0FP48
ENSG00000267645	ENST00000476151.5 link	n.*612C>T		non_coding_transcript_exon_variant	Exon 8 of 9	1		ENSP00000418603.1
ENSG00000205236	ENST00000519541.1 link	n.670C>T		non_coding_transcript_exon_variant	Exon 5 of 26	2		ENSP00000429397.1	A0A286YEE6
ENSG00000267645	ENST00000476151.5 link	n.*612C>T		3_prime_UTR_variant	Exon 8 of 9	1		ENSP00000418603.1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

146700

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000348

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000138

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000114

AC:

AN:

967610

Hom.:

Cov.:

AF XY:

0.0000125

AC XY:

AN XY:

480896

show subpopulations

Gnomad4 AFR exome

AF:

0.000408

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000136

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000109

AC:

AN:

146814

Hom.:

Cov.:

AF XY:

0.000126

AC XY:

AN XY:

71386

show subpopulations

Gnomad4 AFR

AF:

0.000347

Gnomad4 AMR

AF:

0.000137

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000169

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Oct 20, 2023

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.670C>T (p.L224F) alteration is located in exon 5 (coding exon 5) of the UPK3BL gene. This alteration results from a C to T substitution at nucleotide position 670, causing the leucine (L) at amino acid position 224 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.13

BayesDel_noAF

Benign

-0.43

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.033

Eigen

Benign

-0.39

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.11

M_CAP

Uncertain

0.12

MetaRNN

Benign

0.16

MetaSVM

Benign

-0.82

MutationAssessor

Benign

2.0

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-1.5

REVEL

Benign

0.040

Sift

Benign

0.17

Sift4G

Uncertain

0.032

Vest4

0.35

MutPred

0.34

Loss of helix (P = 0.2271);

MVP

0.061

ClinPred

0.19

GERP RS

-0.20

Varity_R

0.098

gMVP

0.30

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over