dbSNP rs9366778: LINC02571:n.171+76C>T (chr6-31301396-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 ENST00000539514.1(LINC02571):n.171+76C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 150,880 control chromosomes in the GnomAD database, including 17,537 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 0.47 ( 17536 hom., cov: 31)

Exomes 𝑓: 0.40 ( 1 hom. )

Consequence

LINC02571
ENST00000539514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.913

Publications

39 publications found

Variant links:

Genes affected

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

LINC02571 links:

ENSG00000298396 (HGNC:):

ENSG00000298396 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.6 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02571	NR_149115.1 link	n.166+76C>T		intron_variant	Intron 1 of 3
LOC112267902	XR_926691.3 link	n.1060+363C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02571	ENST00000539514.1 link	n.171+76C>T		intron_variant	Intron 1 of 3	4
ENSG00000298396	ENST00000755297.1 link	n.32+30290G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.473

AC:

71321

AN:

150752

Hom.:

17513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.549

Gnomad ASJ

AF:

0.396

Gnomad EAS

AF:

0.617

Gnomad SAS

AF:

0.609

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.400

AC:

AN:

Hom.:

AF XY:

0.400

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.375

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.375

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.473

AC:

71395

AN:

150870

Hom.:

17536

Cov.:

AF XY:

0.483

AC XY:

35596

AN XY:

73700

show subpopulations

African (AFR)

AF:

0.532

AC:

21860

AN:

41062

American (AMR)

AF:

0.550

AC:

8355

AN:

15196

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

1359

AN:

3434

East Asian (EAS)

AF:

0.618

AC:

3172

AN:

5134

South Asian (SAS)

AF:

0.609

AC:

2917

AN:

4788

European-Finnish (FIN)

AF:

0.516

AC:

5390

AN:

10454

Middle Eastern (MID)

AF:

0.579

AC:

169

AN:

292

European-Non Finnish (NFE)

AF:

0.398

AC:

26847

AN:

67510

Other (OTH)

AF:

0.494

AC:

1039

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1820

3641

5461

7282

9102

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

654

1308

1962

2616

3270

<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:

0.435

Hom.:

34146

Bravo

AF:

0.477

Asia WGS

AF:

0.618

AC:

2149

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

7.1

(source)

DANN

Benign

0.29

PhyloP100

-0.91

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over