dbSNP rs10211524: LINC02245:n.513+67014C>T (chr2-64980940-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 ENST00000653778.1(LINC02245):n.513+67014C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,086 control chromosomes in the GnomAD database, including 21,343 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 0.51 ( 21343 hom., cov: 33)

Consequence

LINC02245
ENST00000653778.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45

Publications

30 publications found

Variant links:

Genes affected

LINC02245 (HGNC:53134): (long intergenic non-protein coding RNA 2245)

LINC02245 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02245	ENST00000653778.1 link	n.513+67014C>T	intron_variant	Intron 2 of 3
LINC02245	ENST00000669631.1 link	n.227-10155C>T	intron_variant	Intron 1 of 4
LINC02245	ENST00000771808.1 link	n.574-24956C>T	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78217

AN:

151966

Hom.:

21318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.654

Gnomad AMI

AF:

0.380

Gnomad AMR

AF:

0.599

Gnomad ASJ

AF:

0.427

Gnomad EAS

AF:

0.809

Gnomad SAS

AF:

0.357

Gnomad FIN

AF:

0.410

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.423

Gnomad OTH

AF:

0.512

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

GnomAD4 genome

AF:

0.515

AC:

78288

AN:

152086

Hom.:

21343

Cov.:

AF XY:

0.515

AC XY:

38310

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.653

AC:

27101

AN:

41480

American (AMR)

AF:

0.599

AC:

9167

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.427

AC:

1483

AN:

3470

East Asian (EAS)

AF:

0.809

AC:

4193

AN:

5184

South Asian (SAS)

AF:

0.355

AC:

1713

AN:

4826

European-Finnish (FIN)

AF:

0.410

AC:

4336

AN:

10566

Middle Eastern (MID)

AF:

0.432

AC:

127

AN:

294

European-Non Finnish (NFE)

AF:

0.423

AC:

28745

AN:

67958

Other (OTH)

AF:

0.512

AC:

1076

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1856

3712

5567

7423

9279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

676

1352

2028

2704

3380

<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:

0.438

Hom.:

7204

Bravo

AF:

0.544

Asia WGS

AF:

0.570

AC:

1981

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.17

(source)

DANN

Benign

0.72

PhyloP100

-2.5

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