Genetic Variant ENST00000439421.2:n.24-730C>T (chr10-130482151-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 ENST00000439421.2(LINC02646):n.24-730C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,224 control chromosomes in the GnomAD database, including 2,218 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 0.15 ( 2218 hom., cov: 33)

Consequence

LINC02646
ENST00000439421.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

3 publications found

Variant links:

Genes affected

LINC02646 (HGNC:54130): (long intergenic non-protein coding RNA 2646)

LINC02646 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=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.366 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
LINC02646	ENST00000439421.2 link	n.24-730C>T	intron_variant	Intron 1 of 1	3
LINC02646	ENST00000648275.1 link	n.504-730C>T	intron_variant	Intron 1 of 1
LINC02646	ENST00000657871.1 link	n.553-730C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

23118

AN:

152106

Hom.:

2210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.207

Gnomad AMI

AF:

0.0592

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.0989

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.0909

Gnomad OTH

AF:

0.150

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

GnomAD4 genome

AF:

0.152

AC:

23160

AN:

152224

Hom.:

2218

Cov.:

AF XY:

0.156

AC XY:

11596

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.207

AC:

8604

AN:

41536

American (AMR)

AF:

0.239

AC:

3652

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.112

AC:

388

AN:

3470

East Asian (EAS)

AF:

0.380

AC:

1964

AN:

5164

South Asian (SAS)

AF:

0.186

AC:

897

AN:

4818

European-Finnish (FIN)

AF:

0.0989

AC:

1050

AN:

10620

Middle Eastern (MID)

AF:

0.180

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0909

AC:

6181

AN:

68002

Other (OTH)

AF:

0.150

AC:

317

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

980

1959

2939

3918

4898

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.132

Hom.:

4149

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.13

(source)

DANN

Benign

0.72

PhyloP100

-1.5

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