Genetic Variant LUCAT1:n.464-17539T>A (chr5-91262549-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000647807.1(LUCAT1):n.464-17539T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 151,906 control chromosomes in the GnomAD database, including 49,373 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 49373 hom., cov: 29)

Consequence

LUCAT1
ENST00000647807.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.73

Publications

2 publications found

Variant links:

Genes affected

LUCAT1 (HGNC:48498): (lung cancer associated transcript 1)

LUCAT1 links:

LOC107986432 (HGNC:):

LOC107986432 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.05).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986432	XR_001742795.2 link	n.611+2114T>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LUCAT1	ENST00000647807.1 link	n.464-17539T>A	intron_variant	Intron 2 of 6
LUCAT1	ENST00000648385.1 link	n.367+51089T>A	intron_variant	Intron 2 of 5
LUCAT1	ENST00000648822.1 link	n.487+2114T>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.800

AC:

121463

AN:

151786

Hom.:

49343

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.909

Gnomad AMR

AF:

0.747

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.753

Gnomad FIN

AF:

0.888

Gnomad MID

AF:

0.823

Gnomad NFE

AF:

0.874

Gnomad OTH

AF:

0.812

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

GnomAD4 genome

AF:

0.800

AC:

121544

AN:

151906

Hom.:

49373

Cov.:

AF XY:

0.799

AC XY:

59286

AN XY:

74210

show subpopulations

African (AFR)

AF:

0.702

AC:

29052

AN:

41384

American (AMR)

AF:

0.747

AC:

11398

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.908

AC:

3149

AN:

3468

East Asian (EAS)

AF:

0.536

AC:

2741

AN:

5112

South Asian (SAS)

AF:

0.751

AC:

3621

AN:

4822

European-Finnish (FIN)

AF:

0.888

AC:

9386

AN:

10570

Middle Eastern (MID)

AF:

0.816

AC:

240

AN:

294

European-Non Finnish (NFE)

AF:

0.874

AC:

59417

AN:

67972

Other (OTH)

AF:

0.811

AC:

1715

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1145

2289

3434

4578

5723

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

880

1760

2640

3520

4400

<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:

0.820

Hom.:

2717

Bravo

AF:

0.784

Asia WGS

AF:

0.658

AC:

2290

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.44

(source)

DANN

Benign

0.35

PhyloP100

-2.7

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over