Genetic Variant LINC03004:n.433+27279T>G (chr6-137701403-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000646621.1(LINC03004):n.601+12714T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,056 control chromosomes in the GnomAD database, including 18,558 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 0.48 ( 18558 hom., cov: 32)

Consequence

LINC03004
ENST00000646621.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.30

Variant links:

Genes affected

LINC03004 (HGNC:56128): (long intergenic non-protein coding RNA 3004)

LINC03004 links:

ENSG00000303318 (HGNC:):

ENSG00000303318 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=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC03004	ENST00000635999.1 link	n.433+27279T>G	intron_variant	Intron 2 of 2	5
LINC03004	ENST00000646621.1 link	n.601+12714T>G	intron_variant	Intron 4 of 4
ENSG00000303318	ENST00000793597.1 link	n.305-1874A>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.483

AC:

73332

AN:

151938

Hom.:

18550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.320

Gnomad AMR

AF:

0.444

Gnomad ASJ

AF:

0.380

Gnomad EAS

AF:

0.798

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.472

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.400

Gnomad OTH

AF:

0.489

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

GnomAD4 genome

AF:

0.482

AC:

73366

AN:

152056

Hom.:

18558

Cov.:

AF XY:

0.486

AC XY:

36133

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.613

AC:

25435

AN:

41476

American (AMR)

AF:

0.443

AC:

6765

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.380

AC:

1317

AN:

3470

East Asian (EAS)

AF:

0.798

AC:

4129

AN:

5176

South Asian (SAS)

AF:

0.434

AC:

2091

AN:

4816

European-Finnish (FIN)

AF:

0.472

AC:

4987

AN:

10560

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.400

AC:

27203

AN:

67974

Other (OTH)

AF:

0.483

AC:

1020

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1879

3757

5636

7514

9393

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.425

Hom.:

57672

Bravo

AF:

0.486

Asia WGS

AF:

0.593

AC:

2061

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.76

(source)

DANN

Benign

0.73

PhyloP100

-1.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Loading publications...

6-137701403-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

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