Genetic Variant LUCAT1:n.873-1534C>T (chr5-91204234-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The XR_001742795.2(LOC107986432):n.1021-1534C>T 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. 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

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 ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Benign. The variant received -12 points.

Show applied only (2)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).
	BA1Stand-alone benign allele frequency (>5%)		GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.4637 — exceeds 5%% threshold (BA1 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

Gene / Transcript	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
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.

Publications

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CA123062477

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence

Publications

Other links and lift over

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

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