Genetic Variant LINC02608:n.153-4045C>T (chr1-212218821-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 ENST00000685933.2(LINC02608):n.153-4045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 152,018 control chromosomes in the GnomAD database, including 11,436 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 0.38 ( 11436 hom., cov: 32)

Consequence

LINC02608
ENST00000685933.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.520

Publications

16 publications found

Variant links:

Genes affected

LINC02608 (HGNC:54052): (long intergenic non-protein coding RNA 2608)

LINC02608 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02608	NR_125982.1 link	n.292-4045C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02608	ENST00000685933.2 link	n.153-4045C>T	intron_variant	Intron 2 of 4
LINC02608	ENST00000771310.1 link	n.163-4045C>T	intron_variant	Intron 2 of 3
LINC02608	ENST00000771311.1 link	n.184-4045C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.383

AC:

58183

AN:

151900

Hom.:

11423

Cov.:

show subpopulations

Gnomad AFR

AF:

0.435

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.326

Gnomad ASJ

AF:

0.318

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.290

Gnomad NFE

AF:

0.403

Gnomad OTH

AF:

0.377

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

GnomAD4 genome

AF:

0.383

AC:

58232

AN:

152018

Hom.:

11436

Cov.:

AF XY:

0.374

AC XY:

27827

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.435

AC:

18031

AN:

41440

American (AMR)

AF:

0.326

AC:

4977

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.318

AC:

1104

AN:

3472

East Asian (EAS)

AF:

0.206

AC:

1068

AN:

5178

South Asian (SAS)

AF:

0.325

AC:

1567

AN:

4818

European-Finnish (FIN)

AF:

0.271

AC:

2858

AN:

10556

Middle Eastern (MID)

AF:

0.291

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.403

AC:

27414

AN:

67954

Other (OTH)

AF:

0.377

AC:

794

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1797

3593

5390

7186

8983

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.385

Hom.:

9053

Bravo

AF:

0.389

Asia WGS

AF:

0.285

AC:

992

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.9

(source)

DANN

Benign

0.28

PhyloP100

0.52

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