dbSNP rs668103: LINC00571:n.389-37381T>G (chr13-38180613-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000451826.2(LINC00571):n.389-37381T>G 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 151,938 control chromosomes in the GnomAD database, including 9,023 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 ( 9023 hom., cov: 32)

Consequence

LINC00571
ENST00000451826.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

1 publications found

Variant links:

Genes affected

LINC00571 (HGNC:43721): (long intergenic non-protein coding RNA 571)

LINC00571 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00571	ENST00000451826.2 link	n.389-37381T>G	intron_variant	Intron 2 of 7	2
LINC00571	ENST00000454060.2 link	n.442+10245T>G	intron_variant	Intron 3 of 7	3
LINC00571	ENST00000700975.1 link	n.424+10245T>G	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51292

AN:

151818

Hom.:

9004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.372

Gnomad ASJ

AF:

0.358

Gnomad EAS

AF:

0.435

Gnomad SAS

AF:

0.478

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.343

Gnomad OTH

AF:

0.325

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

GnomAD4 genome

AF:

0.338

AC:

51348

AN:

151938

Hom.:

9023

Cov.:

AF XY:

0.344

AC XY:

25579

AN XY:

74270

show subpopulations

African (AFR)

AF:

0.272

AC:

11271

AN:

41490

American (AMR)

AF:

0.372

AC:

5687

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.358

AC:

1240

AN:

3464

East Asian (EAS)

AF:

0.434

AC:

2233

AN:

5142

South Asian (SAS)

AF:

0.480

AC:

2318

AN:

4828

European-Finnish (FIN)

AF:

0.405

AC:

4271

AN:

10552

Middle Eastern (MID)

AF:

0.265

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.343

AC:

23303

AN:

67880

Other (OTH)

AF:

0.330

AC:

696

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1693

3386

5079

6772

8465

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

536

1072

1608

2144

2680

<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:

0.350

Hom.:

5426

Bravo

AF:

0.329

Asia WGS

AF:

0.457

AC:

1588

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

5.4

(source)

DANN

Benign

0.45

PhyloP100

1.2

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