Genetic Variant LINC00299:n.444+1827C>T (chr2-8390126-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 ENST00000655671.1(LINC00299):n.444+1827C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,014 control chromosomes in the GnomAD database, including 9,728 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 0.35 ( 9728 hom., cov: 31)

Consequence

LINC00299
ENST00000655671.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0140

Publications

14 publications found

Variant links:

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

LINC00299 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00299	ENST00000655671.1 link	n.444+1827C>T	intron_variant	Intron 3 of 6
LINC00299	ENST00000661371.1 link	n.485+1827C>T	intron_variant	Intron 3 of 5
LINC00299	ENST00000669954.1 link	n.571+1827C>T	intron_variant	Intron 3 of 7

Frequencies

GnomAD3 genomes

AF:

0.348

AC:

52857

AN:

151896

Hom.:

9723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.232

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.336

Gnomad EAS

AF:

0.381

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.332

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

GnomAD4 genome

AF:

0.348

AC:

52896

AN:

152014

Hom.:

9728

Cov.:

AF XY:

0.355

AC XY:

26348

AN XY:

74310

show subpopulations

African (AFR)

AF:

0.232

AC:

9611

AN:

41412

American (AMR)

AF:

0.371

AC:

5665

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.336

AC:

1163

AN:

3462

East Asian (EAS)

AF:

0.380

AC:

1968

AN:

5174

South Asian (SAS)

AF:

0.411

AC:

1982

AN:

4818

European-Finnish (FIN)

AF:

0.479

AC:

5066

AN:

10586

Middle Eastern (MID)

AF:

0.306

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26281

AN:

67972

Other (OTH)

AF:

0.329

AC:

694

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1721

3442

5163

6884

8605

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

534

1068

1602

2136

2670

<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:

0.369

Hom.:

31202

Bravo

AF:

0.333

Asia WGS

AF:

0.387

AC:

1348

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.2

(source)

DANN

Benign

0.66

PhyloP100

-0.014

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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