Genetic Variant ENSG00000257060:n.546-64311C>T (chr15-93465926-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 ENST00000543286.5(ENSG00000257060):n.546-64311C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0412 in 152,126 control chromosomes in the GnomAD database, including 352 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 0.041 ( 352 hom., cov: 32)

Consequence

ENSG00000257060
ENST00000543286.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.73

Publications

0 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.266 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.546-64311C>T	intron_variant	Intron 2 of 3	2
ENSG00000257060	ENST00000553478.1 link	n.319-91546C>T	intron_variant	Intron 2 of 3	4
ENSG00000257060	ENST00000554105.6 link	n.499-64311C>T	intron_variant	Intron 3 of 5	4

Frequencies

GnomAD3 genomes

AF:

0.0411

AC:

6242

AN:

152008

Hom.:

344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0145

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.0775

Gnomad ASJ

AF:

0.0306

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.0745

Gnomad FIN

AF:

0.0402

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0299

Gnomad OTH

AF:

0.0421

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

GnomAD4 genome

AF:

0.0412

AC:

6262

AN:

152126

Hom.:

352

Cov.:

AF XY:

0.0437

AC XY:

3253

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.0145

AC:

601

AN:

41496

American (AMR)

AF:

0.0782

AC:

1195

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0306

AC:

106

AN:

3468

East Asian (EAS)

AF:

0.277

AC:

1429

AN:

5150

South Asian (SAS)

AF:

0.0737

AC:

355

AN:

4814

European-Finnish (FIN)

AF:

0.0402

AC:

425

AN:

10578

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0299

AC:

2034

AN:

68012

Other (OTH)

AF:

0.0492

AC:

104

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

278

556

835

1113

1391

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

228

304

380

<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:

0.0349

Hom.:

219

Bravo

AF:

0.0461

Asia WGS

AF:

0.188

AC:

655

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.12

(source)

DANN

Benign

0.59

PhyloP100

-4.7

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