Genetic Variant ENSG00000257548:n.128-3582G>T (chr12-107118391-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000547679.1(ENSG00000257548):n.128-3582G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,182 control chromosomes in the GnomAD database, including 2,399 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 0.17 ( 2399 hom., cov: 32)

Consequence

ENSG00000257548
ENST00000547679.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.115

Publications

4 publications found

Variant links:

Genes affected

ENSG00000257548 (HGNC:):

ENSG00000257548 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257548	ENST00000547679.1 link	n.128-3582G>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.173

AC:

26328

AN:

152064

Hom.:

2390

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.154

Gnomad ASJ

AF:

0.110

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.157

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.173

AC:

26366

AN:

152182

Hom.:

2399

Cov.:

AF XY:

0.174

AC XY:

12933

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.146

AC:

6061

AN:

41530

American (AMR)

AF:

0.153

AC:

2346

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.110

AC:

381

AN:

3468

East Asian (EAS)

AF:

0.294

AC:

1516

AN:

5162

South Asian (SAS)

AF:

0.193

AC:

931

AN:

4820

European-Finnish (FIN)

AF:

0.157

AC:

1662

AN:

10592

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12927

AN:

67996

Other (OTH)

AF:

0.181

AC:

381

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1107

2213

3320

4426

5533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

296

592

888

1184

1480

<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:

0.167

Hom.:

1388

Bravo

AF:

0.171

Asia WGS

AF:

0.264

AC:

918

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

9.7

(source)

DANN

Benign

0.76

PhyloP100

0.12

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