Genetic Variant LINC02571:n.242-97A>G (chr6-31294392-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000539514.1(LINC02571):n.242-97A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,080 control chromosomes in the GnomAD database, including 9,570 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 ( 9570 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

LINC02571
ENST00000539514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.03

Publications

38 publications found

Variant links:

Genes affected

LINC02571 (HGNC:53630): (long intergenic non-protein coding RNA 2571)

LINC02571 links:

ENSG00000298396 (HGNC:):

ENSG00000298396 links:

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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 = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1 link	n.237-97A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1 link	n.242-97A>G		intron_variant	Intron 2 of 3	4
ENSG00000298396	ENST00000755297.1 link	n.32+23286T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53090

AN:

151962

Hom.:

9558

Cov.:

show subpopulations

Gnomad AFR

AF:

0.446

Gnomad AMI

AF:

0.288

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.392

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.347

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

GnomAD4 genome

AF:

0.349

AC:

53133

AN:

152080

Hom.:

9570

Cov.:

AF XY:

0.352

AC XY:

26197

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.446

AC:

18489

AN:

41472

American (AMR)

AF:

0.334

AC:

5095

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1031

AN:

3466

East Asian (EAS)

AF:

0.307

AC:

1586

AN:

5174

South Asian (SAS)

AF:

0.331

AC:

1593

AN:

4816

European-Finnish (FIN)

AF:

0.392

AC:

4151

AN:

10588

Middle Eastern (MID)

AF:

0.350

AC:

103

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20099

AN:

67980

Other (OTH)

AF:

0.344

AC:

724

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1759

3518

5276

7035

8794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.312

Hom.:

32724

Bravo

AF:

0.348

Asia WGS

AF:

0.311

AC:

1083

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

6.8

(source)

DANN

Benign

0.50

PhyloP100

-1.0

Splicing

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

Publications

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6-31294392-T-C

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