dbSNP rs7336525: LINC00539:n.349C>T (chr13-21344705-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 ENST00000411525.1(LINC00539):n.349C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 166,768 control chromosomes in the GnomAD database, including 35,023 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 0.63 ( 30901 hom., cov: 33)

Exomes 𝑓: 0.75 ( 4122 hom. )

Consequence

LINC00539
ENST00000411525.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.250

Publications

7 publications found

Variant links:

Genes affected

LINC00539 (HGNC:43672): (long intergenic non-protein coding RNA 539)

LINC00539 links:

ENSG00000291046 (HGNC:):

ENSG00000291046 links:

MIPEPP3 (HGNC:39458): (mitochondrial intermediate peptidase pseudogene 3)

MIPEPP3 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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00539	NR_103840.1 link	n.82C>T	non_coding_transcript_exon_variant	Exon 1 of 6
LINC00539	NR_103841.1 link	n.155C>T	non_coding_transcript_exon_variant	Exon 1 of 3
MIPEPP3	NR_046461.1 link	n.439-6443G>A	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00539	ENST00000411525.1 link	n.349C>T	non_coding_transcript_exon_variant	Exon 3 of 5	3
LINC00539	ENST00000423575.6 link	n.350C>T	non_coding_transcript_exon_variant	Exon 1 of 3	3
LINC00539	ENST00000434601.7 link	n.349C>T	non_coding_transcript_exon_variant	Exon 3 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.631

AC:

95860

AN:

151976

Hom.:

30885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.625

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.663

Gnomad SAS

AF:

0.717

Gnomad FIN

AF:

0.751

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.679

Gnomad OTH

AF:

0.623

GnomAD4 exome

AF:

0.749

AC:

10995

AN:

14674

Hom.:

4122

Cov.:

AF XY:

0.751

AC XY:

5229

AN XY:

6966

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.751

AC:

10823

AN:

14418

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.694

AC:

AN:

134

Other (OTH)

AF:

0.660

AC:

AN:

106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

126

252

377

503

629

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.631

AC:

95917

AN:

152094

Hom.:

30901

Cov.:

AF XY:

0.635

AC XY:

47225

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.488

AC:

20241

AN:

41466

American (AMR)

AF:

0.686

AC:

10489

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

2124

AN:

3470

East Asian (EAS)

AF:

0.663

AC:

3424

AN:

5162

South Asian (SAS)

AF:

0.716

AC:

3451

AN:

4818

European-Finnish (FIN)

AF:

0.751

AC:

7950

AN:

10584

Middle Eastern (MID)

AF:

0.592

AC:

174

AN:

294

European-Non Finnish (NFE)

AF:

0.679

AC:

46166

AN:

67974

Other (OTH)

AF:

0.628

AC:

1328

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1831

3662

5492

7323

9154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

780

1560

2340

3120

3900

<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:

0.663

Hom.:

22500

Bravo

AF:

0.616

Asia WGS

AF:

0.679

AC:

2361

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

2.6

(source)

DANN

Benign

0.60

PhyloP100

0.25

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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