Genetic Variant ENSG00000297367:n.278+24400G>A (chr1-36524039-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000747486.1(ENSG00000297367):n.278+24400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,258 control chromosomes in the GnomAD database, including 1,122 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 0.11 ( 1122 hom., cov: 33)

Consequence

ENSG00000297367
ENST00000747486.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.27

Publications

4 publications found

Variant links:

Genes affected

ENSG00000297367 (HGNC:):

ENSG00000297367 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=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297367	ENST00000747486.1 link	n.278+24400G>A	intron_variant	Intron 3 of 3
ENSG00000297367	ENST00000747487.1 link	n.363-32597G>A	intron_variant	Intron 1 of 2
ENSG00000297367	ENST00000747488.1 link	n.211-3442G>A	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.110

AC:

16726

AN:

152140

Hom.:

1123

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0336

Gnomad AMI

AF:

0.0768

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.132

Gnomad EAS

AF:

0.0296

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.167

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.133

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

GnomAD4 genome

AF:

0.110

AC:

16720

AN:

152258

Hom.:

1122

Cov.:

AF XY:

0.112

AC XY:

8344

AN XY:

74452

show subpopulations

African (AFR)

AF:

0.0335

AC:

1393

AN:

41562

American (AMR)

AF:

0.117

AC:

1787

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.132

AC:

458

AN:

3470

East Asian (EAS)

AF:

0.0291

AC:

151

AN:

5194

South Asian (SAS)

AF:

0.187

AC:

901

AN:

4824

European-Finnish (FIN)

AF:

0.167

AC:

1771

AN:

10576

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.145

AC:

9867

AN:

68022

Other (OTH)

AF:

0.133

AC:

280

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

778

1557

2335

3114

3892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.138

Hom.:

836

Bravo

AF:

0.0988

Asia WGS

AF:

0.137

AC:

475

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

(source)

DANN

Benign

0.60

PhyloP100

3.3

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