Genetic Variant ENST00000770646.1:n.529-38715C>T (chr2-15744432-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 ENST00000770646.1(LINC01804):n.529-38715C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 285,326 control chromosomes in the GnomAD database, including 1,172 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 0.069 ( 1050 hom., cov: 32)

Exomes 𝑓: 0.016 ( 122 hom. )

Consequence

LINC01804
ENST00000770646.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.58

Publications

1 publications found

Variant links:

Genes affected

LINC01804 (HGNC:52596): (long intergenic non-protein coding RNA 1804)

LINC01804 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 (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01804	ENST00000770646.1 link	n.529-38715C>T	intron_variant	Intron 3 of 4
LINC01804	ENST00000770647.1 link	n.407-38715C>T	intron_variant	Intron 2 of 3
LINC01804	ENST00000770648.1 link	n.429+35986C>T	intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes

AF:

0.0691

AC:

10509

AN:

151998

Hom.:

1042

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0391

Gnomad ASJ

AF:

0.0469

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.00270

Gnomad FIN

AF:

0.00774

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.00898

Gnomad OTH

AF:

0.0588

GnomAD4 exome

AF:

0.0159

AC:

2117

AN:

133210

Hom.:

122

AF XY:

0.0140

AC XY:

1036

AN XY:

73864

show subpopulations

African (AFR)

AF:

0.218

AC:

981

AN:

4506

American (AMR)

AF:

0.0210

AC:

192

AN:

9148

Ashkenazi Jewish (ASJ)

AF:

0.0366

AC:

108

AN:

2948

East Asian (EAS)

AF:

0.00

AC:

AN:

7360

South Asian (SAS)

AF:

0.00250

AC:

AN:

24406

European-Finnish (FIN)

AF:

0.00776

AC:

AN:

6440

Middle Eastern (MID)

AF:

0.0508

AC:

AN:

788

European-Non Finnish (NFE)

AF:

0.00780

AC:

555

AN:

71136

Other (OTH)

AF:

0.0201

AC:

130

AN:

6478

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

192

287

383

479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

120

150

<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:

0.0693

AC:

10548

AN:

152116

Hom.:

1050

Cov.:

AF XY:

0.0675

AC XY:

5019

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.216

AC:

8948

AN:

41470

American (AMR)

AF:

0.0390

AC:

597

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0469

AC:

163

AN:

3472

East Asian (EAS)

AF:

0.000194

AC:

AN:

5146

South Asian (SAS)

AF:

0.00249

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.00774

AC:

AN:

10600

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00899

AC:

611

AN:

68000

Other (OTH)

AF:

0.0582

AC:

123

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

426

853

1279

1706

2132

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

208

312

416

520

<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:

0.0486

Hom.:

Bravo

AF:

0.0775

Asia WGS

AF:

0.0230

AC:

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

0.15

(source)

DANN

Benign

0.42

PhyloP100

-2.6

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