Genetic Variant ENSG00000259609:n.54-6582G>A (chr15-84060637-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 ENST00000559921.1(ENSG00000259609):n.54-6582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 150,294 control chromosomes in the GnomAD database, including 911 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 0.098 ( 911 hom., cov: 32)

Consequence

ENSG00000259609
ENST00000559921.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.591

Publications

5 publications found

Variant links:

Genes affected

ENSG00000259609 (HGNC:):

ENSG00000259609 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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
ENSG00000259609	ENST00000559921.1 link	n.54-6582G>A	intron_variant	Intron 1 of 1	6
ENSG00000296726	ENST00000741322.1 link	n.143+19408G>A	intron_variant	Intron 1 of 1
ENSG00000296726	ENST00000741323.1 link	n.98-10859G>A	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.0975

AC:

14643

AN:

150176

Hom.:

909

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0344

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.0748

Gnomad ASJ

AF:

0.0887

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.0720

Gnomad FIN

AF:

0.150

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.108

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

GnomAD4 genome

AF:

0.0976

AC:

14662

AN:

150294

Hom.:

911

Cov.:

AF XY:

0.0969

AC XY:

7120

AN XY:

73448

show subpopulations

African (AFR)

AF:

0.0345

AC:

1423

AN:

41300

American (AMR)

AF:

0.0747

AC:

1132

AN:

15144

Ashkenazi Jewish (ASJ)

AF:

0.0887

AC:

303

AN:

3416

East Asian (EAS)

AF:

0.163

AC:

840

AN:

5158

South Asian (SAS)

AF:

0.0729

AC:

349

AN:

4790

European-Finnish (FIN)

AF:

0.150

AC:

1539

AN:

10258

Middle Eastern (MID)

AF:

0.113

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.130

AC:

8722

AN:

66926

Other (OTH)

AF:

0.112

AC:

235

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

670

1340

2009

2679

3349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

170

340

510

680

850

<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:

0.119

Hom.:

609

Bravo

AF:

0.0880

Asia WGS

AF:

0.148

AC:

513

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

(source)

DANN

Benign

0.69

PhyloP100

-0.59

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