dbSNP rs565738: LINC00571:n.323-28131C>T (chr13-38256214-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 ENST00000451826.2(LINC00571):n.323-28131C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0337 in 152,220 control chromosomes in the GnomAD database, including 195 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 0.034 ( 195 hom., cov: 32)

Consequence

LINC00571
ENST00000451826.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.50

Publications

0 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0902 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.323-28131C>T	intron_variant	Intron 1 of 7	2
LINC00571	ENST00000454060.2 link	n.323-28131C>T	intron_variant	Intron 1 of 7	3
LINC00571	ENST00000700975.1 link	n.305-28131C>T	intron_variant	Intron 1 of 8

Frequencies

GnomAD3 genomes

AF:

0.0337

AC:

5119

AN:

152102

Hom.:

195

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0925

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0157

Gnomad ASJ

AF:

0.0433

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0394

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00889

Gnomad OTH

AF:

0.0244

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

GnomAD4 genome

AF:

0.0337

AC:

5134

AN:

152220

Hom.:

195

Cov.:

AF XY:

0.0328

AC XY:

2443

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0926

AC:

3848

AN:

41542

American (AMR)

AF:

0.0156

AC:

239

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0433

AC:

150

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.0390

AC:

188

AN:

4820

European-Finnish (FIN)

AF:

0.00292

AC:

AN:

10602

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00890

AC:

605

AN:

68010

Other (OTH)

AF:

0.0241

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

238

475

713

950

1188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<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:

0.0328

Hom.:

Bravo

AF:

0.0360

Asia WGS

AF:

0.0230

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.5

(source)

DANN

Benign

0.46

PhyloP100

1.5

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