Genetic Variant ENST00000655671.1:n.49-26082C>T (chr2-8419050-G-A) – 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.49-26082C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0712 in 152,236 control chromosomes in the GnomAD database, including 594 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 0.071 ( 594 hom., cov: 31)

Consequence

LINC00299
ENST00000655671.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.695

Publications

0 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 (EAS) allele frequency at 95% confidence interval = 0.263 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.49-26082C>T	intron_variant	Intron 1 of 6
LINC00299	ENST00000657091.2 link	n.60-26082C>T	intron_variant	Intron 1 of 3
LINC00299	ENST00000661371.1 link	n.90-26082C>T	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.0712

AC:

10824

AN:

152118

Hom.:

592

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0172

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0917

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.275

Gnomad SAS

AF:

0.0859

Gnomad FIN

AF:

0.117

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0740

Gnomad OTH

AF:

0.0852

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

GnomAD4 genome

AF:

0.0712

AC:

10842

AN:

152236

Hom.:

594

Cov.:

AF XY:

0.0753

AC XY:

5606

AN XY:

74436

show subpopulations

African (AFR)

AF:

0.0172

AC:

714

AN:

41552

American (AMR)

AF:

0.0920

AC:

1407

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

394

AN:

3470

East Asian (EAS)

AF:

0.275

AC:

1425

AN:

5186

South Asian (SAS)

AF:

0.0862

AC:

416

AN:

4826

European-Finnish (FIN)

AF:

0.117

AC:

1236

AN:

10588

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0740

AC:

5031

AN:

67998

Other (OTH)

AF:

0.0890

AC:

188

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

490

980

1471

1961

2451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<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:

0.0684

Hom.:

274

Bravo

AF:

0.0674

Asia WGS

AF:

0.186

AC:

645

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

3.8

(source)

DANN

Benign

0.39

PhyloP100

0.69

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