Genetic Variant ENSG00000296268:n.51-17122G>A (chr7-25092760-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 ENST00000737690.1(ENSG00000296268):n.51-17122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,570 control chromosomes in the GnomAD database, including 3,769 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 0.22 ( 3769 hom., cov: 31)

Consequence

ENSG00000296268
ENST00000737690.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.113

Publications

3 publications found

Variant links:

COSMIC-nc: COSV70884489

Genes affected

ENSG00000296268 (HGNC:):

ENSG00000296268 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=-0.96).

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	Effect	Exon rank
ENSG00000296268	ENST00000737690.1 link	n.51-17122G>A	intron_variant	Intron 1 of 5
ENSG00000296268	ENST00000737691.1 link	n.211+7647G>A	intron_variant	Intron 2 of 5
ENSG00000296268	ENST00000737692.1 link	n.52-17122G>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33125

AN:

151466

Hom.:

3766

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.182

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.317

Gnomad SAS

AF:

0.250

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.287

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.215

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

GnomAD4 genome

AF:

0.219

AC:

33141

AN:

151570

Hom.:

3769

Cov.:

AF XY:

0.222

AC XY:

16440

AN XY:

74044

show subpopulations

African (AFR)

AF:

0.157

AC:

6472

AN:

41350

American (AMR)

AF:

0.268

AC:

4088

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

725

AN:

3468

East Asian (EAS)

AF:

0.316

AC:

1630

AN:

5152

South Asian (SAS)

AF:

0.250

AC:

1196

AN:

4792

European-Finnish (FIN)

AF:

0.250

AC:

2594

AN:

10366

Middle Eastern (MID)

AF:

0.286

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.232

AC:

15739

AN:

67896

Other (OTH)

AF:

0.213

AC:

448

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1275

2549

3824

5098

6373

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.227

Hom.:

15558

Bravo

AF:

0.214

Asia WGS

AF:

0.228

AC:

794

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

3.2

(source)

DANN

Benign

0.76

PhyloP100

-0.11

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