Genetic Variant LINC01724:n.130+45008G>A (chr1-196115362-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 ENST00000838209.1(LINC01724):n.130+45008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,154 control chromosomes in the GnomAD database, including 1,130 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 0.12 ( 1130 hom., cov: 32)

Consequence

LINC01724
ENST00000838209.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.926

Publications

4 publications found

Variant links:

Genes affected

LINC01724 (HGNC:52512): (long intergenic non-protein coding RNA 1724)

LINC01724 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.227 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
LINC01724	ENST00000838209.1 link	n.130+45008G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.116

AC:

17595

AN:

152036

Hom.:

1125

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.166

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.169

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.112

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

GnomAD4 genome

AF:

0.116

AC:

17617

AN:

152154

Hom.:

1130

Cov.:

AF XY:

0.120

AC XY:

8897

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.103

AC:

4289

AN:

41532

American (AMR)

AF:

0.105

AC:

1598

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

410

AN:

3468

East Asian (EAS)

AF:

0.166

AC:

860

AN:

5170

South Asian (SAS)

AF:

0.238

AC:

1146

AN:

4814

European-Finnish (FIN)

AF:

0.169

AC:

1786

AN:

10588

Middle Eastern (MID)

AF:

0.151

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.105

AC:

7141

AN:

67994

Other (OTH)

AF:

0.117

AC:

248

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

788

1576

2363

3151

3939

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.114

Hom.:

547

Bravo

AF:

0.108

Asia WGS

AF:

0.228

AC:

790

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

(source)

DANN

Benign

0.45

PhyloP100

0.93

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