ENST00000647807.1:n.873-1534C>T

Variant names:

• chr5-91204234-G-A
• rs116743293
• ENST00000647807.1:n.873-1534C>T

GermlineCancer (beta)

Variant summary

Our verdict is Likely benign.

-4 Likely Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received -4 classification points (ACGS-UK Somatic Oncogenicity v2025). B1_Strong

The ENST00000647807.1(LUCAT1):n.873-1534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: ENST00000647807.1 is not a MANE Select or MANE Plus Clinical transcript for LUCAT1; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.394 (AC=20,773) in the gnomAD database across 52,702 control chromosomes, including 9,150 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.464. 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: 𝑓 0.39 (9150 hom., cov: 0)
• Consequence: LUCAT1 ENST00000647807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 0 publications found

Genes affected

LUCAT1 (HGNC:48498): ()

LOC107986432 (HGNC:):

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Likely_benign. The variant received -4 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	B1High frequency in general population		GnomAD effective popmax AF >1% — B1 stand-alone benign; GnomAD effective popmax AF = 0.464 — exceeds 1% threshold (B1 applied)

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

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

LUCAT1 ENST00000647807.1

HGVSc / HGVSpn.873-1534C>T

Exon rankIntron 5 of 6

intron

Prot:

LUCAT1 ENST00000648385.1

HGVSc / HGVSpn.524-1534C>T

Exon rankIntron 3 of 5

intron

Prot:

LUCAT1 ENST00000649322.1

HGVSc / HGVSpn.566+38707C>T

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: 0.394	AC:20724	Hom:9132	AN:52590	Cov:0
GnomAD4 genome	AF: 0.394	AC:20773	Hom:9150	AN:52702	Cov:0
TOPMed (Bravo)	AF: 0.397	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.129	AC:612	Hom:120	AN:4758	Cov:
Local & regional cohorts 3 sources Population-specific and national genomic databases
Denmark Genome	AF: 0.0433	AC:13	Hom:	AN:300	Cov:
GenomeAsia100K	AF: 0.232	AC:341	Hom:	AN:1466	Cov:
Qatari Genome	AF: 0.273	AC:18	Hom:	AN:66	Cov:

Showing 7 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	Prediction
AlphaGenome AVI	Benign	3.3
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.3
DANN	Benign	0.36
GPN-Star LLR	N/A	-1.7
GPN-Star score	N/A	1.7
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.

Other links and lift over

dbSNP: rs116743293;

hg19: chr5-90500051;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar