Genetic Variant LINC02756:n.312-2957G>A (chr11-91836654-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 ENST00000671523.1(LINC02756):n.312-2957G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 152,076 control chromosomes in the GnomAD database, including 96 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 0.019 ( 96 hom., cov: 32)

Consequence

LINC02756
ENST00000671523.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0380

Publications

1 publications found

Variant links:

Genes affected

LINC02756 (HGNC:54276): (long intergenic non-protein coding RNA 2756)

LINC02756 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 (AMR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02756	NR_187308.1 link	n.314-2957G>A	intron_variant	Intron 3 of 11
LINC02756	NR_187309.1 link	n.415-2957G>A	intron_variant	Intron 4 of 13
LINC02756	NR_187310.1 link	n.307-4931G>A	intron_variant	Intron 3 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02756	ENST00000671523.1 link	n.312-2957G>A		intron_variant	Intron 3 of 11
LINC02756	ENST00000797231.1 link	n.172-19315G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0186

AC:

2834

AN:

151958

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00328

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0915

Gnomad ASJ

AF:

0.00606

Gnomad EAS

AF:

0.0487

Gnomad SAS

AF:

0.0102

Gnomad FIN

AF:

0.0248

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0103

Gnomad OTH

AF:

0.00957

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

GnomAD4 genome

AF:

0.0187

AC:

2841

AN:

152076

Hom.:

Cov.:

AF XY:

0.0212

AC XY:

1579

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.00328

AC:

136

AN:

41524

American (AMR)

AF:

0.0918

AC:

1402

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00606

AC:

AN:

3468

East Asian (EAS)

AF:

0.0490

AC:

250

AN:

5102

South Asian (SAS)

AF:

0.0104

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.0248

AC:

263

AN:

10596

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0103

AC:

699

AN:

67970

Other (OTH)

AF:

0.00947

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

143

285

428

570

713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0165

Hom.:

117

Bravo

AF:

0.0227

Asia WGS

AF:

0.0190

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.9

(source)

DANN

Benign

0.65

PhyloP100

-0.038

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