Genetic Variant ENST00000543286.5:n.546-36778A>G (chr15-93493459-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000543286.5(ENSG00000257060):n.546-36778A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,116 control chromosomes in the GnomAD database, including 6,857 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 0.27 ( 6857 hom., cov: 32)

Consequence

ENSG00000257060
ENST00000543286.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.47

Publications

11 publications found

Variant links:

Genes affected

ENSG00000257060 (HGNC:):

ENSG00000257060 links:

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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 = 0.448 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
ENSG00000257060	ENST00000543286.5 link	n.546-36778A>G	intron_variant	Intron 2 of 3	2
ENSG00000257060	ENST00000553478.1 link	n.319-64013A>G	intron_variant	Intron 2 of 3	4
ENSG00000257060	ENST00000554105.6 link	n.499-36778A>G	intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.265

AC:

40291

AN:

151998

Hom.:

6843

Cov.:

show subpopulations

Gnomad AFR

AF:

0.449

Gnomad AMI

AF:

0.251

Gnomad AMR

AF:

0.280

Gnomad ASJ

AF:

0.140

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.410

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.270

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

GnomAD4 genome

AF:

0.265

AC:

40350

AN:

152116

Hom.:

6857

Cov.:

AF XY:

0.270

AC XY:

20095

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.449

AC:

18616

AN:

41476

American (AMR)

AF:

0.280

AC:

4277

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.140

AC:

484

AN:

3468

East Asian (EAS)

AF:

0.463

AC:

2396

AN:

5172

South Asian (SAS)

AF:

0.409

AC:

1974

AN:

4828

European-Finnish (FIN)

AF:

0.174

AC:

1840

AN:

10584

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.145

AC:

9888

AN:

68008

Other (OTH)

AF:

0.268

AC:

565

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1377

2755

4132

5510

6887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

406

812

1218

1624

2030

<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:

0.201

Hom.:

7893

Bravo

AF:

0.280

Asia WGS

AF:

0.452

AC:

1571

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.041

(source)

DANN

Benign

0.76

PhyloP100

-2.5

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