Genetic Variant ENSG00000302043:n.245-4325T>G (chr6-27747464-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000783576.1(ENSG00000302043):n.245-4325T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,028 control chromosomes in the GnomAD database, including 9,983 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 0.33 ( 9983 hom., cov: 32)

Consequence

ENSG00000302043
ENST00000783576.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

18 publications found

Variant links:

COSMIC-nc: COSV69399382

Genes affected

ENSG00000302043 (HGNC:):

ENSG00000302043 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000302043	ENST00000783576.1 link	n.245-4325T>G	intron_variant	Intron 1 of 4
ENSG00000302043	ENST00000783577.1 link	n.203+6595T>G	intron_variant	Intron 1 of 2
ENSG00000302043	ENST00000783578.1 link	n.191-4325T>G	intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.330

AC:

50114

AN:

151910

Hom.:

9957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.561

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.247

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.215

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.314

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

GnomAD4 genome

AF:

0.330

AC:

50184

AN:

152028

Hom.:

9983

Cov.:

AF XY:

0.324

AC XY:

24105

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.561

AC:

23235

AN:

41412

American (AMR)

AF:

0.292

AC:

4464

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.164

AC:

570

AN:

3470

East Asian (EAS)

AF:

0.195

AC:

1009

AN:

5182

South Asian (SAS)

AF:

0.247

AC:

1194

AN:

4828

European-Finnish (FIN)

AF:

0.191

AC:

2014

AN:

10568

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.245

AC:

16623

AN:

67964

Other (OTH)

AF:

0.311

AC:

656

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1542

3084

4625

6167

7709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.282

Hom.:

14916

Bravo

AF:

0.349

Asia WGS

AF:

0.245

AC:

853

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.5

(source)

DANN

Benign

0.43

PhyloP100

-1.0

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