Genetic Variant LINC03004:n.105+4221G>A (chr6-137652212-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000746620.1(LINC03004):n.105+4221G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0891 in 152,228 control chromosomes in the GnomAD database, including 646 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 0.089 ( 646 hom., cov: 31)

Consequence

LINC03004
ENST00000746620.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.690

Publications

5 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=-0.87).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.103 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
LINC03004	ENST00000746620.1 link	n.105+4221G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0890

AC:

13543

AN:

152110

Hom.:

642

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0936

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.107

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.0711

Gnomad FIN

AF:

0.0835

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0880

Gnomad OTH

AF:

0.0890

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

GnomAD4 genome

AF:

0.0891

AC:

13558

AN:

152228

Hom.:

646

Cov.:

AF XY:

0.0893

AC XY:

6644

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0934

AC:

3878

AN:

41542

American (AMR)

AF:

0.107

AC:

1643

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

474

AN:

3464

East Asian (EAS)

AF:

0.00154

AC:

AN:

5186

South Asian (SAS)

AF:

0.0720

AC:

347

AN:

4818

European-Finnish (FIN)

AF:

0.0835

AC:

885

AN:

10602

Middle Eastern (MID)

AF:

0.0680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0880

AC:

5985

AN:

67998

Other (OTH)

AF:

0.0885

AC:

187

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

610

1219

1829

2438

3048

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0841

Hom.:

385

Bravo

AF:

0.0927

Asia WGS

AF:

0.0420

AC:

146

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

5.1

(source)

DANN

Benign

0.67

PhyloP100

0.69

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