dbSNP rs9619497: LINC02885:n.202+22460C>T (chr22-34975259-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 ENST00000668433.1(LINC02885):n.202+22460C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,000 control chromosomes in the GnomAD database, including 6,348 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 0.29 ( 6348 hom., cov: 32)

Consequence

LINC02885
ENST00000668433.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

4 publications found

Variant links:

Genes affected

LINC02885 (HGNC:41188): (long intergenic non-protein coding RNA 2885)

LINC02885 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02885	NR_138042.1 link	n.198+22460C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02885	ENST00000668433.1 link	n.202+22460C>T	intron_variant	Intron 2 of 3
LINC02885	ENST00000700833.2 link	n.95+22460C>T	intron_variant	Intron 1 of 3
LINC02885	ENST00000754702.1 link	n.365+22460C>T	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.285

AC:

43342

AN:

151882

Hom.:

6349

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.222

Gnomad EAS

AF:

0.390

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.270

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

GnomAD4 genome

AF:

0.285

AC:

43349

AN:

152000

Hom.:

6348

Cov.:

AF XY:

0.283

AC XY:

21004

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.336

AC:

13932

AN:

41456

American (AMR)

AF:

0.311

AC:

4749

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

771

AN:

3470

East Asian (EAS)

AF:

0.389

AC:

2001

AN:

5150

South Asian (SAS)

AF:

0.172

AC:

826

AN:

4808

European-Finnish (FIN)

AF:

0.250

AC:

2639

AN:

10546

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.258

AC:

17532

AN:

67970

Other (OTH)

AF:

0.266

AC:

561

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

1527

3055

4582

6110

7637

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

434

868

1302

1736

2170

<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:

0.269

Hom.:

11158

Bravo

AF:

0.294

Asia WGS

AF:

0.259

AC:

901

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.056

(source)

DANN

Benign

0.53

PhyloP100

-1.1

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