Genetic Variant ENSG00000259789:n.1922G>A (chr14-90489716-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 ENST00000567837.1(ENSG00000259789):n.1922G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 152,150 control chromosomes in the GnomAD database, including 26,000 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 0.57 ( 25996 hom., cov: 33)

Exomes 𝑓: 0.50 ( 4 hom. )

Consequence

ENSG00000259789
ENST00000567837.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.526

Publications

5 publications found

Variant links:

Genes affected

ENSG00000259789 (HGNC:):

ENSG00000259789 links:

LINC00642 (HGNC:44293): (long intergenic non-protein coding RNA 642)

LINC00642 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.706 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567837.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000259789	ENST00000567837.1	TSL:6	n.1922G>A	non_coding_transcript_exon	Exon 1 of 1
ENSG00000259789	ENST00000647570.1		n.391G>A	non_coding_transcript_exon	Exon 4 of 4
LINC00642	ENST00000655041.1		n.304-17C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87243

AN:

152002

Hom.:

25945

Cov.:

show subpopulations

Gnomad AFR

AF:

0.702

Gnomad AMI

AF:

0.287

Gnomad AMR

AF:

0.662

Gnomad ASJ

AF:

0.567

Gnomad EAS

AF:

0.725

Gnomad SAS

AF:

0.609

Gnomad FIN

AF:

0.495

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.478

Gnomad OTH

AF:

0.593

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.455

AC XY:

AN XY:

show subpopulations

African (AFR)

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:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.574

AC:

87359

AN:

152120

Hom.:

25996

Cov.:

AF XY:

0.581

AC XY:

43172

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.703

AC:

29176

AN:

41520

American (AMR)

AF:

0.663

AC:

10137

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

1969

AN:

3470

East Asian (EAS)

AF:

0.725

AC:

3742

AN:

5162

South Asian (SAS)

AF:

0.608

AC:

2931

AN:

4818

European-Finnish (FIN)

AF:

0.495

AC:

5241

AN:

10586

Middle Eastern (MID)

AF:

0.558

AC:

163

AN:

292

European-Non Finnish (NFE)

AF:

0.478

AC:

32490

AN:

67966

Other (OTH)

AF:

0.593

AC:

1249

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1871

3742

5614

7485

9356

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<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:

0.511

Hom.:

57319

Bravo

AF:

0.591

Asia WGS

AF:

0.649

AC:

2258

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

4.4

(source)

DANN

Benign

0.72

PhyloP100

-0.53

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over