Genetic Variant ENST00000411525.1: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

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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