Genetic Variant ENST00000503048.1:n.91+62659G>A (chr5-153160794-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

-12

BP4_StrongBA1

The ENST00000503048.1(LINC01470):n.91+62659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,746 control chromosomes in the GnomAD database, including 21,453 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 0.52 ( 21453 hom., cov: 31)

Consequence

LINC01470
ENST00000503048.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.467

Publications

17 publications found

Variant links:

Genes affected

LINC01470 (HGNC:51105): (long intergenic non-protein coding RNA 1470)

LINC01470 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01470	ENST00000503048.1 link	n.91+62659G>A		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79360

AN:

151628

Hom.:

21431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.422

Gnomad AMI

AF:

0.638

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.824

Gnomad SAS

AF:

0.669

Gnomad FIN

AF:

0.570

Gnomad MID

AF:

0.516

Gnomad NFE

AF:

0.521

Gnomad OTH

AF:

0.508

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

GnomAD4 genome

AF:

0.523

AC:

79422

AN:

151746

Hom.:

21453

Cov.:

AF XY:

0.530

AC XY:

39329

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.422

AC:

17431

AN:

41312

American (AMR)

AF:

0.621

AC:

9458

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.534

AC:

1854

AN:

3470

East Asian (EAS)

AF:

0.825

AC:

4255

AN:

5160

South Asian (SAS)

AF:

0.670

AC:

3224

AN:

4814

European-Finnish (FIN)

AF:

0.570

AC:

5996

AN:

10520

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.521

AC:

35394

AN:

67920

Other (OTH)

AF:

0.511

AC:

1081

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1855

3710

5565

7420

9275

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

696

1392

2088

2784

3480

<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:

0.528

Hom.:

33975

Bravo

AF:

0.522

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

(source)

DANN

Benign

0.61

PhyloP100

-0.47

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