Genetic Variant ENST00000420395.1:n.33-48A>G (chr10-7469641-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 ENST00000420395.1(LINC02642):n.33-48A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0528 in 152,274 control chromosomes in the GnomAD database, including 308 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 0.053 ( 308 hom., cov: 32)

Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

LINC02642
ENST00000420395.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0710

Publications

0 publications found

Variant links:

Genes affected

LINC02642 (HGNC:54124): (long intergenic non-protein coding RNA 2642)

LINC02642 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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.079 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02642	NR_184107.1 link	n.81-48A>G	intron_variant	Intron 1 of 3
LINC02642	NR_184108.1 link	n.81-48A>G	intron_variant	Intron 1 of 2
LINC02642	NR_184109.1 link	n.81-48A>G	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02642	ENST00000420395.1 link	n.33-48A>G	intron_variant	Intron 1 of 3	3
LINC02642	ENST00000660269.1 link	n.111-48A>G	intron_variant	Intron 1 of 4
LINC02642	ENST00000670632.2 link	n.186+45A>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0528

AC:

8040

AN:

152150

Hom.:

307

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0145

Gnomad AMI

AF:

0.161

Gnomad AMR

AF:

0.0582

Gnomad ASJ

AF:

0.0865

Gnomad EAS

AF:

0.00192

Gnomad SAS

AF:

0.0851

Gnomad FIN

AF:

0.0294

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.0762

Gnomad OTH

AF:

0.0722

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.167

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0528

AC:

8038

AN:

152268

Hom.:

308

Cov.:

AF XY:

0.0521

AC XY:

3883

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.0144

AC:

599

AN:

41560

American (AMR)

AF:

0.0581

AC:

888

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0865

AC:

300

AN:

3470

East Asian (EAS)

AF:

0.00193

AC:

AN:

5184

South Asian (SAS)

AF:

0.0858

AC:

414

AN:

4826

European-Finnish (FIN)

AF:

0.0294

AC:

312

AN:

10622

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0762

AC:

5182

AN:

68000

Other (OTH)

AF:

0.0715

AC:

151

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

396

792

1187

1583

1979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

180

270

360

450

<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:

0.0719

Hom.:

801

Bravo

AF:

0.0528

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

4.5

(source)

DANN

Benign

0.76

PhyloP100

0.071

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