Genetic Variant ENST00000737486.1:n.121+7199delT (chr12-102551564-AT-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000737486.1(ENSG00000296233):n.121+7199delT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.92 ( 65103 hom., cov: 0)

Consequence

ENSG00000296233
ENST00000737486.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.182

Publications

1 publications found

Variant links:

COSMIC-nc: COSV65887918

Genes affected

ENSG00000296233 (HGNC:):

ENSG00000296233 links:

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

LINC02456 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1 link	n.34902+67683delT		intron_variant	Intron 11 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296233	ENST00000737486.1 link	n.121+7199delT		intron_variant	Intron 1 of 3
ENSG00000296233	ENST00000737487.1 link	n.121+7199delT		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.925

AC:

140366

AN:

151788

Hom.:

65043

Cov.:

show subpopulations

Gnomad AFR

AF:

0.983

Gnomad AMI

AF:

0.926

Gnomad AMR

AF:

0.935

Gnomad ASJ

AF:

0.839

Gnomad EAS

AF:

0.951

Gnomad SAS

AF:

0.883

Gnomad FIN

AF:

0.903

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.896

Gnomad OTH

AF:

0.923

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

GnomAD4 genome

AF:

0.925

AC:

140485

AN:

151906

Hom.:

65103

Cov.:

AF XY:

0.925

AC XY:

68604

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.983

AC:

40730

AN:

41426

American (AMR)

AF:

0.935

AC:

14284

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.839

AC:

2914

AN:

3472

East Asian (EAS)

AF:

0.950

AC:

4845

AN:

5098

South Asian (SAS)

AF:

0.883

AC:

4249

AN:

4812

European-Finnish (FIN)

AF:

0.903

AC:

9521

AN:

10538

Middle Eastern (MID)

AF:

0.837

AC:

246

AN:

294

European-Non Finnish (NFE)

AF:

0.896

AC:

60903

AN:

67974

Other (OTH)

AF:

0.924

AC:

1950

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

521

1042

1564

2085

2606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

906

1812

2718

3624

4530

<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:

0.878

Hom.:

2626

Bravo

AF:

0.932

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.18

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