Genetic Variant LINC02715:n.252+8348A>G (chr11-109504243-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 ENST00000532929.1(LINC02715):n.252+8348A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0836 in 152,176 control chromosomes in the GnomAD database, including 910 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 0.084 ( 910 hom., cov: 32)

Consequence

LINC02715
ENST00000532929.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.72

Publications

1 publications found

Variant links:

Genes affected

LINC02715 (HGNC:54232): (long intergenic non-protein coding RNA 2715)

LINC02715 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 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
LINC02715	ENST00000532929.1 link	n.252+8348A>G	intron_variant	Intron 2 of 3	3
LINC02715	ENST00000532992.5 link	n.427+8336A>G	intron_variant	Intron 3 of 4	4
LINC02715	ENST00000818760.1 link	n.672+8336A>G	intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes

AF:

0.0835

AC:

12694

AN:

152058

Hom.:

904

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0653

Gnomad ASJ

AF:

0.0424

Gnomad EAS

AF:

0.00135

Gnomad SAS

AF:

0.00952

Gnomad FIN

AF:

0.0312

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0405

Gnomad OTH

AF:

0.0718

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

GnomAD4 genome

AF:

0.0836

AC:

12728

AN:

152176

Hom.:

910

Cov.:

AF XY:

0.0816

AC XY:

6072

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.198

AC:

8239

AN:

41512

American (AMR)

AF:

0.0653

AC:

997

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0424

AC:

147

AN:

3466

East Asian (EAS)

AF:

0.00155

AC:

AN:

5166

South Asian (SAS)

AF:

0.00953

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0312

AC:

332

AN:

10626

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0405

AC:

2751

AN:

67986

Other (OTH)

AF:

0.0706

AC:

149

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

566

1131

1697

2262

2828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0611

Hom.:

208

Bravo

AF:

0.0926

Asia WGS

AF:

0.0250

AC:

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.25

(source)

DANN

Benign

0.88

PhyloP100

-3.7

Mutation Taster

=100/0

polymorphism

(source)

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