Genetic Variant ENST00000416680.1:n.76+350C>T (chr4-117360214-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 ENST00000416680.1(LINC02262):n.76+350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,896 control chromosomes in the GnomAD database, including 2,987 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 0.19 ( 2987 hom., cov: 32)

Consequence

LINC02262
ENST00000416680.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.829

Publications

3 publications found

Variant links:

Genes affected

LINC02262 (HGNC:53174): (long intergenic non-protein coding RNA 2262)

LINC02262 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02262	NR_147151.1 link	n.76+350C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02262	ENST00000416680.1 link	n.76+350C>T	intron_variant	Intron 1 of 6	3
LINC02262	ENST00000653017.1 link	n.112+330C>T	intron_variant	Intron 1 of 4
LINC02262	ENST00000657433.1 link	n.89+330C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28875

AN:

151780

Hom.:

2983

Cov.:

show subpopulations

Gnomad AFR

AF:

0.148

Gnomad AMI

AF:

0.144

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.297

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.220

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

GnomAD4 genome

AF:

0.190

AC:

28887

AN:

151896

Hom.:

2987

Cov.:

AF XY:

0.192

AC XY:

14279

AN XY:

74180

show subpopulations

African (AFR)

AF:

0.148

AC:

6137

AN:

41454

American (AMR)

AF:

0.148

AC:

2263

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

866

AN:

3470

East Asian (EAS)

AF:

0.420

AC:

2150

AN:

5118

South Asian (SAS)

AF:

0.246

AC:

1183

AN:

4816

European-Finnish (FIN)

AF:

0.238

AC:

2512

AN:

10534

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.193

AC:

13088

AN:

67944

Other (OTH)

AF:

0.223

AC:

470

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1205

2410

3614

4819

6024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

316

632

948

1264

1580

<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:

0.192

Hom.:

12431

Bravo

AF:

0.181

Asia WGS

AF:

0.325

AC:

1126

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.80

(source)

DANN

Benign

0.34

PhyloP100

-0.83

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