Genetic Variant ENST00000549055.1:n.127-496T>C (chr12-30207946-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000549055.1(ENSG00000257262):n.127-496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,282 control chromosomes in the GnomAD database, including 1,000 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 ( 1000 hom., cov: 33)

Consequence

ENSG00000257262
ENST00000549055.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.154

Publications

3 publications found

Variant links:

Genes affected

ENSG00000257262 (HGNC:):

ENSG00000257262 links:

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

LINC02386 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 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
ENSG00000257262	ENST00000549055.1 link	n.127-496T>C	intron_variant	Intron 1 of 2	3
LINC02386	ENST00000824524.1 link	n.170-8307A>G	intron_variant	Intron 2 of 2
LINC02386	ENST00000824525.1 link	n.224-8307A>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.105

AC:

15952

AN:

152164

Hom.:

1000

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0423

Gnomad AMI

AF:

0.179

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.0926

Gnomad EAS

AF:

0.129

Gnomad SAS

AF:

0.0358

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.140

Gnomad OTH

AF:

0.125

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

GnomAD4 genome

AF:

0.105

AC:

15949

AN:

152282

Hom.:

1000

Cov.:

AF XY:

0.103

AC XY:

7660

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.0422

AC:

1754

AN:

41570

American (AMR)

AF:

0.103

AC:

1574

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0926

AC:

321

AN:

3468

East Asian (EAS)

AF:

0.129

AC:

669

AN:

5176

South Asian (SAS)

AF:

0.0358

AC:

173

AN:

4834

European-Finnish (FIN)

AF:

0.143

AC:

1513

AN:

10606

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.140

AC:

9489

AN:

68018

Other (OTH)

AF:

0.125

AC:

264

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

730

1459

2189

2918

3648

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.109

Hom.:

135

Bravo

AF:

0.102

Asia WGS

AF:

0.0830

AC:

286

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

3.7

(source)

DANN

Benign

0.59

PhyloP100

-0.15

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