Genetic Variant LINC02901:n.276-2817T>C (chr6-158945229-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000795721.1(LINC02901):n.276-2817T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,124 control chromosomes in the GnomAD database, including 1,717 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 0.11 ( 1717 hom., cov: 31)

Consequence

LINC02901
ENST00000795721.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.130

Publications

13 publications found

Variant links:

Genes affected

LINC02901 (HGNC:21179): (long intergenic non-protein coding RNA 2901)

LINC02901 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=-0.7).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02901	ENST00000795721.1 link	n.276-2817T>C		intron_variant	Intron 2 of 2
LINC02901	ENST00000795722.1 link	n.502-2817T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17295

AN:

152006

Hom.:

1706

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0748

Gnomad AMI

AF:

0.0516

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0902

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.0758

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.114

AC:

17342

AN:

152124

Hom.:

1717

Cov.:

AF XY:

0.120

AC XY:

8911

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0753

AC:

3125

AN:

41510

American (AMR)

AF:

0.282

AC:

4309

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

376

AN:

3470

East Asian (EAS)

AF:

0.415

AC:

2146

AN:

5168

South Asian (SAS)

AF:

0.194

AC:

933

AN:

4820

European-Finnish (FIN)

AF:

0.0902

AC:

954

AN:

10578

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0758

AC:

5152

AN:

68002

Other (OTH)

AF:

0.129

AC:

272

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

681

1362

2042

2723

3404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.115

Hom.:

518

Bravo

AF:

0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

7.7

(source)

DANN

Benign

0.79

PhyloP100

-0.13

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