dbSNP rs2593270: LINC02375:n.227+3427C>T (chr12-127330633-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 ENST00000545739.2(LINC02375):n.227+3427C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 152,096 control chromosomes in the GnomAD database, including 10,385 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 0.34 ( 10385 hom., cov: 32)

Consequence

LINC02375
ENST00000545739.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

3 publications found

Variant links:

Genes affected

LINC02375 (HGNC:53297): (long intergenic non-protein coding RNA 2375)

LINC02375 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02375	NR_110057.1 link	n.201+3427C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02375	ENST00000545739.2 link	n.227+3427C>T	intron_variant	Intron 2 of 2	1
LINC02375	ENST00000657634.2 link	n.293+3427C>T	intron_variant	Intron 2 of 2
LINC02375	ENST00000670647.2 link	n.281+3427C>T	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51361

AN:

151976

Hom.:

10365

Cov.:

show subpopulations

Gnomad AFR

AF:

0.564

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.210

Gnomad EAS

AF:

0.0335

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.306

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

GnomAD4 genome

AF:

0.338

AC:

51422

AN:

152096

Hom.:

10385

Cov.:

AF XY:

0.332

AC XY:

24720

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.564

AC:

23370

AN:

41440

American (AMR)

AF:

0.299

AC:

4567

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.210

AC:

727

AN:

3468

East Asian (EAS)

AF:

0.0332

AC:

172

AN:

5180

South Asian (SAS)

AF:

0.187

AC:

903

AN:

4822

European-Finnish (FIN)

AF:

0.253

AC:

2684

AN:

10590

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.264

AC:

17972

AN:

67988

Other (OTH)

AF:

0.302

AC:

640

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1615

3230

4845

6460

8075

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

480

960

1440

1920

2400

<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:

0.266

Hom.:

4754

Bravo

AF:

0.353

Asia WGS

AF:

0.142

AC:

496

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.14

(source)

DANN

Benign

0.20

PhyloP100

-0.60

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