Genetic Variant ENSG00000257062:n.*115-1104T>G (chr12-21130019-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000593147.5(ENSG00000257062):n.*115-1104T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,102 control chromosomes in the GnomAD database, including 402 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 0.038 ( 402 hom., cov: 32)

Consequence

ENSG00000257062
ENST00000593147.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.243

Publications

11 publications found

Variant links:

Genes affected

ENSG00000257062 (HGNC:):

ENSG00000257062 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 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
ENSG00000257062	ENST00000593147.5 link	n.*115-1104T>G		intron_variant	Intron 5 of 5	5		ENSP00000467209.1

Frequencies

GnomAD3 genomes

AF:

0.0379

AC:

5762

AN:

151984

Hom.:

401

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0539

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0341

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.0388

Gnomad FIN

AF:

0.0863

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00250

Gnomad OTH

AF:

0.0354

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

GnomAD4 genome

AF:

0.0379

AC:

5771

AN:

152102

Hom.:

402

Cov.:

AF XY:

0.0435

AC XY:

3232

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.0541

AC:

2245

AN:

41512

American (AMR)

AF:

0.0339

AC:

517

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.00663

AC:

AN:

3470

East Asian (EAS)

AF:

0.317

AC:

1635

AN:

5158

South Asian (SAS)

AF:

0.0390

AC:

188

AN:

4816

European-Finnish (FIN)

AF:

0.0863

AC:

914

AN:

10594

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00250

AC:

170

AN:

67990

Other (OTH)

AF:

0.0374

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

241

482

722

963

1204

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<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:

0.0136

Hom.:

667

Bravo

AF:

0.0353

Asia WGS

AF:

0.163

AC:

564

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.2

(source)

DANN

Benign

0.76

PhyloP100

0.24

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