Genetic Variant LINC02984:n.1122A>G (chr8-53516436-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 ENST00000426023.1(LINC02984):n.1122A>G 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 0.376 in 152,106 control chromosomes in the GnomAD database, including 13,007 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 0.38 ( 13004 hom., cov: 32)

Exomes 𝑓: 0.54 ( 3 hom. )

Consequence

LINC02984
ENST00000426023.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.879

Publications

3 publications found

Variant links:

Genes affected

LINC02984 (HGNC:56063): (long intergenic non-protein coding RNA 2984)

LINC02984 links:

ENSG00000308573 (HGNC:):

ENSG00000308573 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=-0.95).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02984	NR_149032.1 link	n.1156A>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124901947	XR_007060913.1 link	n.146-9196T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02984	ENST00000426023.1 link	n.1122A>G	non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC02984	ENST00000656177.1 link	n.1527A>G	non_coding_transcript_exon_variant	Exon 2 of 2
LINC02984	ENST00000670326.1 link	n.1168A>G	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.377

AC:

57259

AN:

151964

Hom.:

13011

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.308

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.537

Gnomad EAS

AF:

0.416

Gnomad SAS

AF:

0.251

Gnomad FIN

AF:

0.479

Gnomad MID

AF:

0.519

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.417

GnomAD4 exome

AF:

0.542

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

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:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.429

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

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:

0.376

AC:

57252

AN:

152082

Hom.:

13004

Cov.:

AF XY:

0.371

AC XY:

27606

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.124

AC:

5162

AN:

41538

American (AMR)

AF:

0.352

AC:

5384

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.537

AC:

1863

AN:

3468

East Asian (EAS)

AF:

0.416

AC:

2146

AN:

5164

South Asian (SAS)

AF:

0.251

AC:

1210

AN:

4820

European-Finnish (FIN)

AF:

0.479

AC:

5053

AN:

10552

Middle Eastern (MID)

AF:

0.510

AC:

150

AN:

294

European-Non Finnish (NFE)

AF:

0.517

AC:

35129

AN:

67950

Other (OTH)

AF:

0.415

AC:

875

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1629

3257

4886

6514

8143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

540

1080

1620

2160

2700

<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:

0.465

Hom.:

54122

Bravo

AF:

0.362

Asia WGS

AF:

0.324

AC:

1128

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.65

(source)

DANN

Benign

0.58

PhyloP100

-0.88

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