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): 0P and 12B. BA1BP4_Strong

The XR_001742795.2(LOC107986432):n.1021-1534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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): (lung cancer associated transcript 1)

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.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LUCAT1	ENST00000647807.1	n.873-1534C>T	intron	N/A
LUCAT1	ENST00000648385.1	n.524-1534C>T	intron	N/A
LUCAT1	ENST00000649322.1	n.566+38707C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

20724

AN:

52590

Hom.:

9132

Cov.:

show subpopulations

Gnomad AFR

AF:

0.471

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.00762

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.255

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.394

AC:

20773

AN:

52702

Hom.:

9150

Cov.:

AF XY:

0.395

AC XY:

10128

AN XY:

25658

show subpopulations

African (AFR)

AF:

0.471

AC:

12258

AN:

26046

American (AMR)

AF:

0.268

AC:

1233

AN:

4596

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

221

AN:

688

East Asian (EAS)

AF:

0.00704

AC:

AN:

1704

South Asian (SAS)

AF:

0.174

AC:

315

AN:

1808

European-Finnish (FIN)

AF:

0.642

AC:

1323

AN:

2060

Middle Eastern (MID)

AF:

0.240

AC:

AN:

100

European-Non Finnish (NFE)

AF:

0.343

AC:

5086

AN:

14836

Other (OTH)

AF:

0.386

AC:

258

AN:

668

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

131

261

392

522

653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

134

268

402

536

670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.131

Hom.:

115

Asia WGS

AF:

0.232

AC:

341

AN:

1466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

3.3

(source)

DANN

Benign

0.36

PhyloP100

0.72

Splicing

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.

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over