Genetic Variant ENST00000440769.4:n.380G>A (chr5-91280763-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 ENST00000440769.4(ENSG00000234292):n.380G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,318 control chromosomes in the GnomAD database, including 52,800 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 0.83 ( 52757 hom., cov: 33)

Exomes 𝑓: 0.94 ( 43 hom. )

Consequence

ENSG00000234292
ENST00000440769.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0940

Publications

4 publications found

Variant links:

Genes affected

ENSG00000234292 (HGNC:):

ENSG00000234292 links:

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=-0.71).

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	TSL
ENSG00000234292	ENST00000440769.4 link	n.380G>A	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000286638	ENST00000660900.3 link	n.619C>T	non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000286638	ENST00000730474.1 link	n.355C>T	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.829

AC:

126072

AN:

152102

Hom.:

52747

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.954

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.912

Gnomad EAS

AF:

0.541

Gnomad SAS

AF:

0.754

Gnomad FIN

AF:

0.894

Gnomad MID

AF:

0.877

Gnomad NFE

AF:

0.876

Gnomad OTH

AF:

0.839

GnomAD4 exome

AF:

0.939

AC:

AN:

Hom.:

Cov.:

AF XY:

0.919

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AF:

0.978

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.977

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.458

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.829

AC:

126128

AN:

152220

Hom.:

52757

Cov.:

AF XY:

0.826

AC XY:

61491

AN XY:

74422

show subpopulations

African (AFR)

AF:

0.793

AC:

32946

AN:

41546

American (AMR)

AF:

0.759

AC:

11613

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.912

AC:

3168

AN:

3472

East Asian (EAS)

AF:

0.541

AC:

2778

AN:

5136

South Asian (SAS)

AF:

0.752

AC:

3636

AN:

4832

European-Finnish (FIN)

AF:

0.894

AC:

9493

AN:

10622

Middle Eastern (MID)

AF:

0.878

AC:

258

AN:

294

European-Non Finnish (NFE)

AF:

0.877

AC:

59602

AN:

67998

Other (OTH)

AF:

0.836

AC:

1764

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1084

2167

3251

4334

5418

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.854

Hom.:

13666

Bravo

AF:

0.816

Asia WGS

AF:

0.667

AC:

2324

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.7

(source)

DANN

Benign

0.91

PhyloP100

0.094

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over