dbSNP rs2829156: LINC01684:n.229-7549C>A (chr21-24538446-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 ENST00000415182.1(LINC01684):n.229-7549C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,040 control chromosomes in the GnomAD database, including 1,676 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 0.14 ( 1676 hom., cov: 32)

Consequence

LINC01684
ENST00000415182.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

1 publications found

Variant links:

Genes affected

LINC01684 (HGNC:52472): (long intergenic non-protein coding RNA 1684)

LINC01684 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01684	NR_135519.1 link	n.270-7549C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01684	ENST00000415182.1 link	n.229-7549C>A	intron_variant	Intron 2 of 2	1
LINC01684	ENST00000655039.1 link	n.168-7549C>A	intron_variant	Intron 2 of 2
LINC01684	ENST00000826644.1 link	n.426-7549C>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20638

AN:

151922

Hom.:

1674

Cov.:

show subpopulations

Gnomad AFR

AF:

0.228

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0828

Gnomad EAS

AF:

0.0561

Gnomad SAS

AF:

0.127

Gnomad FIN

AF:

0.148

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0924

Gnomad OTH

AF:

0.123

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

GnomAD4 genome

AF:

0.136

AC:

20676

AN:

152040

Hom.:

1676

Cov.:

AF XY:

0.136

AC XY:

10128

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.228

AC:

9442

AN:

41438

American (AMR)

AF:

0.124

AC:

1897

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0828

AC:

287

AN:

3468

East Asian (EAS)

AF:

0.0560

AC:

290

AN:

5178

South Asian (SAS)

AF:

0.128

AC:

616

AN:

4822

European-Finnish (FIN)

AF:

0.148

AC:

1560

AN:

10552

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0924

AC:

6284

AN:

67990

Other (OTH)

AF:

0.123

AC:

259

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

906

1812

2718

3624

4530

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

224

448

672

896

1120

<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:

0.108

Hom.:

703

Bravo

AF:

0.138

Asia WGS

AF:

0.102

AC:

355

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.50

(source)

DANN

Benign

0.79

PhyloP100

-1.8

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