ENST00000650150.1:n.380-52046C>T

Variant names:

• chr5-91204234-G-A
• rs116743293
• ENST00000650150.1:n.380-52046C>T

Variant summary

Our verdict is Benign.

<-10 Benign

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

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

The ENST00000650150.1(LUCAT1):n.380-52046C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Note: ENST00000650150.1 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 ENST00000650150.1 intron, non_coding_transcript
• Predictors: AlphaGenome AVI: 3: Benign
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.721
• Publications: 0 publications found

Genes affected

LUCAT1 (HGNC:48498): ()

LOC107986432 (HGNC:):

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

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

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: ENST00000650150.1. 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 ENST00000650150.1		n.380-52046C>T	intronnon_coding_transcript	Intron 3 of 3	Prot:
	LUCAT1 ENST00000647807.1		n.873-1534C>T	intronnon_coding_transcript	Intron 5 of 6	Prot:
	LUCAT1 ENST00000648385.1		n.524-1534C>T	intronnon_coding_transcript	Intron 3 of 5	Prot:

LUCAT1 ENST00000650150.1

HGVSc / HGVSpn.380-52046C>T

Exon rankIntron 3 of 3

intronnon_coding_transcript

Prot:

LUCAT1 ENST00000647807.1

HGVSc / HGVSpn.873-1534C>T

Exon rankIntron 5 of 6

intronnon_coding_transcript

Prot:

LUCAT1 ENST00000648385.1

HGVSc / HGVSpn.524-1534C>T

Exon rankIntron 3 of 5

intronnon_coding_transcript

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

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