Genetic Variant ENST00000647807.1:n.464-23312G>A (chr5-91268322-C-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.464-23312G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 148,204 control chromosomes in the GnomAD database, including 47,330 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 0.79 ( 47330 hom., cov: 25)

Consequence

LUCAT1
ENST00000647807.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.627

Publications

9 publications found

Variant links:

Genes affected

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

LUCAT1 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=-0.7).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LUCAT1	ENST00000647807.1 link	n.464-23312G>A	intron_variant	Intron 2 of 6
LUCAT1	ENST00000648385.1 link	n.367+45316G>A	intron_variant	Intron 2 of 5
LUCAT1	ENST00000648822.1 link	n.437-3609G>A	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.791

AC:

117236

AN:

148128

Hom.:

47318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.664

Gnomad AMI

AF:

0.909

Gnomad AMR

AF:

0.745

Gnomad ASJ

AF:

0.910

Gnomad EAS

AF:

0.536

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.894

Gnomad MID

AF:

0.828

Gnomad NFE

AF:

0.877

Gnomad OTH

AF:

0.811

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

GnomAD4 genome

AF:

0.791

AC:

117278

AN:

148204

Hom.:

47330

Cov.:

AF XY:

0.789

AC XY:

56803

AN XY:

71952

show subpopulations

African (AFR)

AF:

0.664

AC:

26613

AN:

40074

American (AMR)

AF:

0.744

AC:

10967

AN:

14738

Ashkenazi Jewish (ASJ)

AF:

0.910

AC:

3149

AN:

3462

East Asian (EAS)

AF:

0.536

AC:

2725

AN:

5086

South Asian (SAS)

AF:

0.752

AC:

3580

AN:

4762

European-Finnish (FIN)

AF:

0.894

AC:

8258

AN:

9238

Middle Eastern (MID)

AF:

0.821

AC:

230

AN:

280

European-Non Finnish (NFE)

AF:

0.877

AC:

59271

AN:

67606

Other (OTH)

AF:

0.810

AC:

1669

AN:

2060

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1097

2194

3290

4387

5484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

860

1720

2580

3440

4300

<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:

0.827

Hom.:

6820

Bravo

AF:

0.773

Asia WGS

AF:

0.657

AC:

2286

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

4.4

(source)

DANN

Benign

0.77

PhyloP100

-0.63

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