Genetic Variant LUCAT1:n.873-1534C>A (chr5-91204234-G-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is The variant received 0 classification points (ACGS-UK Somatic Oncogenicity v2025).

The XR_001742795.2(LOC107986432):n.1021-1534C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: XR_001742795.2 is not a MANE Select or MANE Plus Clinical transcript for LOC107986432; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. No reliable population frequency data is available for this variant in the gnomAD database. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

LOC107986432
XR_001742795.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.721

Publications

0 publications found

Variant links:

Genes affected

LUCAT1 (HGNC:48498): ()

LUCAT1 links:

LOC107986432 (HGNC:):

LOC107986432 links:

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new If you want to explore the variant's impact on the transcript XR_001742795.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 0 points.

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No applied criteria Uncheck "Show applied only" above to review all 20 criteria.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000647807.1. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

There are no transcript annotations for this variant.

Ensembl Transcripts

Gene / Transcript	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
LUCAT1 ENST00000647807.1	n.873-1534C>A	intron	Intron 5 of 6	Prot:
LUCAT1 ENST00000648385.1	n.524-1534C>A	intron	Intron 3 of 5	Prot:
LUCAT1 ENST00000649322.1	n.566+38707C>A	intron	Intron 4 of 4	Prot:

LUCAT1 ENST00000647807.1

HGVSc / HGVSpn.873-1534C>A

Exon rankIntron 5 of 6

intron

Prot:

LUCAT1 ENST00000648385.1

HGVSc / HGVSpn.524-1534C>A

Exon rankIntron 3 of 5

intron

Prot:

LUCAT1 ENST00000649322.1

HGVSc / HGVSpn.566+38707C>A

Exon rankIntron 4 of 4

intron

Prot:

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 4 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:0
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:0
TOPMed (Bravo) Warning	AF: 0.00000378	AC:1	Hom:0	AN:264690	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:120	AN:4758	Cov:

Showing 4 sources

Tested, but no data found:GnomAD4 exomeIf GnomAD4 is missing, the position is probably not covered by the project.

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score
AlphaGenome AVI	Benign	3.3
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.27
GPN-Star LLR	N/A	-2.1
GPN-Star score	N/A	2.1
PhyloP100	Benign	0.72

Showing 7 of 7 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACGS-UK Somatic Oncogenicity v2025

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence