Genetic Variant ENST00000642830.1:n.38+2055C>A (chr6-137660090-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000642830.1(LINC03004):n.38+2055C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0703 in 152,156 control chromosomes in the GnomAD database, including 576 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 0.070 ( 576 hom., cov: 32)

Consequence

LINC03004
ENST00000642830.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.452

Publications

7 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC03004	ENST00000642830.1 link	n.38+2055C>A	intron_variant	Intron 1 of 6
LINC03004	ENST00000691587.2 link	n.219+2055C>A	intron_variant	Intron 1 of 4
LINC03004	ENST00000692965.3 link	n.61+2055C>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0703

AC:

10689

AN:

152038

Hom.:

575

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0507

Gnomad ASJ

AF:

0.0285

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.0928

Gnomad FIN

AF:

0.0441

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0359

Gnomad OTH

AF:

0.0594

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

GnomAD4 genome

AF:

0.0703

AC:

10702

AN:

152156

Hom.:

576

Cov.:

AF XY:

0.0707

AC XY:

5258

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.126

AC:

5223

AN:

41476

American (AMR)

AF:

0.0508

AC:

777

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0285

AC:

AN:

3472

East Asian (EAS)

AF:

0.205

AC:

1058

AN:

5166

South Asian (SAS)

AF:

0.0933

AC:

449

AN:

4814

European-Finnish (FIN)

AF:

0.0441

AC:

467

AN:

10600

Middle Eastern (MID)

AF:

0.0544

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0359

AC:

2440

AN:

68014

Other (OTH)

AF:

0.0583

AC:

123

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

476

953

1429

1906

2382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

256

384

512

640

<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:

0.0559

Hom.:

600

Bravo

AF:

0.0718

Asia WGS

AF:

0.142

AC:

492

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.1

(source)

DANN

Benign

0.68

PhyloP100

-0.45

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