dbSNP rs17459885: ENSG00000257262: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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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