dbSNP rs73009150: LINC02151:n.486G>A (chr11-116497358-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000452629.3(LINC02151):n.486G>A 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 0.0342 in 152,328 control chromosomes in the GnomAD database, including 119 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 ( 119 hom., cov: 33)

Exomes 𝑓: 0.10 ( 0 hom. )

Consequence

LINC02151
ENST00000452629.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.550

Publications

2 publications found

Variant links:

Genes affected

LINC02151 (HGNC:53013): (long intergenic non-protein coding RNA 2151)

LINC02151 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=-0.87).

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0341 (5200/152280) while in subpopulation NFE AF = 0.0501 (3404/67966). AF 95% confidence interval is 0.0487. There are 119 homozygotes in GnomAd4. There are 2499 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 119 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02151	NR_174967.1 link	n.515G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02151	ENST00000452629.3 link	n.486G>A	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC02151	ENST00000815587.1 link	n.91+3184G>A	intron_variant	Intron 1 of 2
LINC02151	ENST00000815590.1 link	n.113+3184G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0342

AC:

5200

AN:

152162

Hom.:

119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00772

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.0336

Gnomad ASJ

AF:

0.0344

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00600

Gnomad FIN

AF:

0.0592

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0501

Gnomad OTH

AF:

0.0440

GnomAD4 exome

AF:

0.104

AC:

AN:

Hom.:

Cov.:

AF XY:

0.0333

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.435

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:

0.0341

AC:

5200

AN:

152280

Hom.:

119

Cov.:

AF XY:

0.0336

AC XY:

2499

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.00769

AC:

320

AN:

41586

American (AMR)

AF:

0.0335

AC:

513

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.0344

AC:

119

AN:

3460

East Asian (EAS)

AF:

0.000193

AC:

AN:

5186

South Asian (SAS)

AF:

0.00600

AC:

AN:

4832

European-Finnish (FIN)

AF:

0.0592

AC:

629

AN:

10622

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0501

AC:

3404

AN:

67966

Other (OTH)

AF:

0.0435

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

263

525

788

1050

1313

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:

0.0446

Hom.:

132

Bravo

AF:

0.0323

Asia WGS

AF:

0.00404

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

1.3

(source)

DANN

Benign

0.66

PhyloP100

-0.55

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