dbSNP rs7581641: LINC00299:n.48+2026G>A (chr2-8485976-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 ENST00000655671.1(LINC00299):n.48+2026G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,208 control chromosomes in the GnomAD database, including 1,692 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 0.10 ( 1692 hom., cov: 32)

Consequence

LINC00299
ENST00000655671.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.61

Publications

4 publications found

Variant links:

Genes affected

LINC00299 (HGNC:27940): (long intergenic non-protein coding RNA 299)

LINC00299 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00299	ENST00000655671.1 link	n.48+2026G>A	intron_variant	Intron 1 of 6
LINC00299	ENST00000657091.2 link	n.59+89390G>A	intron_variant	Intron 1 of 3
LINC00299	ENST00000661371.1 link	n.89+2026G>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15363

AN:

152090

Hom.:

1683

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0586

Gnomad ASJ

AF:

0.0458

Gnomad EAS

AF:

0.0449

Gnomad SAS

AF:

0.0928

Gnomad FIN

AF:

0.0268

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0270

Gnomad OTH

AF:

0.0934

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

GnomAD4 genome

AF:

0.101

AC:

15412

AN:

152208

Hom.:

1692

Cov.:

AF XY:

0.101

AC XY:

7547

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.273

AC:

11318

AN:

41478

American (AMR)

AF:

0.0586

AC:

897

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.0458

AC:

159

AN:

3470

East Asian (EAS)

AF:

0.0448

AC:

232

AN:

5182

South Asian (SAS)

AF:

0.0923

AC:

445

AN:

4822

European-Finnish (FIN)

AF:

0.0268

AC:

285

AN:

10616

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0270

AC:

1835

AN:

68018

Other (OTH)

AF:

0.0986

AC:

208

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

593

1186

1778

2371

2964

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0499

Hom.:

273

Bravo

AF:

0.109

Asia WGS

AF:

0.109

AC:

381

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.038

(source)

DANN

Benign

0.30

PhyloP100

-3.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs7581641

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