Genetic Variant XR_001742795.1:n.38-1534C>T (chr5-91204234-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The XR_001742795.2(LOC107986432):n.1021-1534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.39 ( 9150 hom., cov: 0)

Consequence

LOC107986432
XR_001742795.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.721

Variant links:

Genes affected

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

LUCAT1 links:

LOC107986432 (HGNC:):

LOC107986432 links:

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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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986432	XR_001742795.2 link	n.1021-1534C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LUCAT1	ENST00000647807.1 link	n.873-1534C>T	intron_variant	Intron 5 of 6
LUCAT1	ENST00000648385.1 link	n.524-1534C>T	intron_variant	Intron 3 of 5
LUCAT1	ENST00000649322.1 link	n.566+38707C>T	intron_variant	Intron 4 of 4

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

Alfa

AF:

0.131

Hom.:

115

Asia WGS

AF:

0.232

AC:

341

AN:

1466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

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XR_001742795.1:n.38-1534C>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over