Genetic Variant LINC00648:n.243+42695A>G (chr14-47857929-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000802535.1(LINC00648):n.243+42695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 151,948 control chromosomes in the GnomAD database, including 45,589 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 0.77 ( 45589 hom., cov: 32)

Consequence

LINC00648
ENST00000802535.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.348

Publications

4 publications found

Variant links:

Genes affected

LINC00648 (HGNC:44302): (long intergenic non-protein coding RNA 648)

LINC00648 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=-0.62).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00648	ENST00000802535.1 link	n.243+42695A>G	intron_variant	Intron 2 of 3
LINC00648	ENST00000802536.1 link	n.129+43597A>G	intron_variant	Intron 1 of 2
LINC00648	ENST00000802537.1 link	n.239+42695A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.769

AC:

116690

AN:

151830

Hom.:

45570

Cov.:

show subpopulations

Gnomad AFR

AF:

0.639

Gnomad AMI

AF:

0.802

Gnomad AMR

AF:

0.761

Gnomad ASJ

AF:

0.819

Gnomad EAS

AF:

0.590

Gnomad SAS

AF:

0.838

Gnomad FIN

AF:

0.790

Gnomad MID

AF:

0.889

Gnomad NFE

AF:

0.851

Gnomad OTH

AF:

0.765

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

GnomAD4 genome

AF:

0.768

AC:

116764

AN:

151948

Hom.:

45589

Cov.:

AF XY:

0.764

AC XY:

56746

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.639

AC:

26478

AN:

41432

American (AMR)

AF:

0.761

AC:

11606

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.819

AC:

2839

AN:

3466

East Asian (EAS)

AF:

0.590

AC:

3025

AN:

5130

South Asian (SAS)

AF:

0.838

AC:

4045

AN:

4828

European-Finnish (FIN)

AF:

0.790

AC:

8354

AN:

10570

Middle Eastern (MID)

AF:

0.881

AC:

259

AN:

294

European-Non Finnish (NFE)

AF:

0.851

AC:

57816

AN:

67950

Other (OTH)

AF:

0.764

AC:

1611

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1315

2629

3944

5258

6573

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:

0.798

Hom.:

6020

Bravo

AF:

0.757

Asia WGS

AF:

0.687

AC:

2388

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

(source)

DANN

Benign

0.66

PhyloP100

0.35

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