dbSNP rs2168784: LINC01324:n.76+31458G>A (chr3-164872151-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 ENST00000497379.3(LINC01324):n.76+31458G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,044 control chromosomes in the GnomAD database, including 7,407 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 0.23 ( 7407 hom., cov: 32)

Consequence

LINC01324
ENST00000497379.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0460

Publications

8 publications found

Variant links:

Genes affected

LINC01324 (HGNC:50530): (long intergenic non-protein coding RNA 1324)

LINC01324 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.559 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
LINC01324	ENST00000497379.3 link	n.76+31458G>A	intron_variant	Intron 1 of 4	5
LINC01324	ENST00000715736.1 link	n.209+26272G>A	intron_variant	Intron 3 of 7
LINC01324	ENST00000722128.1 link	n.539+26272G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35191

AN:

151926

Hom.:

7384

Cov.:

show subpopulations

Gnomad AFR

AF:

0.565

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.113

Gnomad ASJ

AF:

0.0909

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.0520

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.109

Gnomad OTH

AF:

0.185

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

GnomAD4 genome

AF:

0.232

AC:

35251

AN:

152044

Hom.:

7407

Cov.:

AF XY:

0.224

AC XY:

16617

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.565

AC:

23431

AN:

41438

American (AMR)

AF:

0.113

AC:

1722

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0909

AC:

315

AN:

3466

East Asian (EAS)

AF:

0.108

AC:

562

AN:

5182

South Asian (SAS)

AF:

0.144

AC:

694

AN:

4818

European-Finnish (FIN)

AF:

0.0520

AC:

550

AN:

10582

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.109

AC:

7422

AN:

67968

Other (OTH)

AF:

0.182

AC:

385

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1060

2120

3181

4241

5301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

318

636

954

1272

1590

<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:

0.147

Hom.:

4427

Bravo

AF:

0.252

Asia WGS

AF:

0.127

AC:

440

AN:

3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.8

(source)

DANN

Benign

0.36

PhyloP100

0.046

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