dbSNP rs10499194: LINC03004:n.433+7376C>T (chr6-137681500-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000635999.1(LINC03004):n.433+7376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,452 control chromosomes in the GnomAD database, including 4,590 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 0.24 ( 4590 hom., cov: 29)

Consequence

LINC03004
ENST00000635999.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.426

Publications

135 publications found

Variant links:

Genes affected

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

LINC03004 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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.28 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+7376C>T	intron_variant	Intron 2 of 2	5
LINC03004	ENST00000638039.2 link	n.439-5594C>T	intron_variant	Intron 2 of 4	5
LINC03004	ENST00000646621.1 link	n.415-5594C>T	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.238

AC:

35944

AN:

151332

Hom.:

4586

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.401

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.356

Gnomad EAS

AF:

0.0392

Gnomad SAS

AF:

0.257

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.237

AC:

35954

AN:

151452

Hom.:

4590

Cov.:

AF XY:

0.235

AC XY:

17420

AN XY:

73982

show subpopulations

African (AFR)

AF:

0.171

AC:

7065

AN:

41232

American (AMR)

AF:

0.287

AC:

4350

AN:

15156

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

1234

AN:

3468

East Asian (EAS)

AF:

0.0389

AC:

201

AN:

5164

South Asian (SAS)

AF:

0.258

AC:

1230

AN:

4774

European-Finnish (FIN)

AF:

0.224

AC:

2346

AN:

10480

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.274

AC:

18577

AN:

67866

Other (OTH)

AF:

0.239

AC:

503

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1342

2685

4027

5370

6712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

372

744

1116

1488

1860

<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:

0.256

Hom.:

14148

Bravo

AF:

0.242

Asia WGS

AF:

0.148

AC:

517

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.9

(source)

DANN

Benign

0.65

PhyloP100

-0.43

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