Genetic Variant ENSG00000257042:n.320+50947G>T (chr12-27862037-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 ENST00000825469.1(ENSG00000257042):n.320+50947G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,148 control chromosomes in the GnomAD database, including 1,516 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 0.12 ( 1516 hom., cov: 32)

Consequence

ENSG00000257042
ENST00000825469.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.73

Publications

28 publications found

Variant links:

Genes affected

ENSG00000257042 (HGNC:):

ENSG00000257042 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000257042	ENST00000825469.1 link	n.320+50947G>T	intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1 link	n.175+50947G>T	intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1 link	n.140+50947G>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18489

AN:

152030

Hom.:

1514

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0310

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0878

Gnomad FIN

AF:

0.161

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.186

Gnomad OTH

AF:

0.107

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

GnomAD4 genome

AF:

0.122

AC:

18487

AN:

152148

Hom.:

1516

Cov.:

AF XY:

0.117

AC XY:

8737

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0309

AC:

1284

AN:

41524

American (AMR)

AF:

0.105

AC:

1602

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

407

AN:

3472

East Asian (EAS)

AF:

0.00116

AC:

AN:

5172

South Asian (SAS)

AF:

0.0889

AC:

429

AN:

4826

European-Finnish (FIN)

AF:

0.161

AC:

1703

AN:

10572

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.186

AC:

12617

AN:

67980

Other (OTH)

AF:

0.106

AC:

224

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

820

1640

2461

3281

4101

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.151

Hom.:

1058

Bravo

AF:

0.114

Asia WGS

AF:

0.0410

AC:

146

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

(source)

DANN

Benign

0.62

PhyloP100

1.7

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