Genetic Variant ENST00000598433.5:n.354-5436A>G (chr7-80339203-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000598433.5(ENSG00000232667):n.354-5436A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 137,042 control chromosomes in the GnomAD database, including 20,863 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 0.54 ( 20863 hom., cov: 29)

Consequence

ENSG00000232667
ENST00000598433.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Publications

5 publications found

Variant links:

Genes affected

ENSG00000232667 (HGNC:):

ENSG00000232667 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000232667	ENST00000598433.5 link	n.354-5436A>G	intron_variant	Intron 3 of 6	5
ENSG00000232667	ENST00000601205.5 link	n.381-276A>G	intron_variant	Intron 3 of 3	5
ENSG00000232667	ENST00000614372.5 link	n.1061-7835A>G	intron_variant	Intron 6 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.543

AC:

74382

AN:

136918

Hom.:

20825

Cov.:

show subpopulations

Gnomad AFR

AF:

0.793

Gnomad AMI

AF:

0.327

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.376

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.458

Gnomad MID

AF:

0.628

Gnomad NFE

AF:

0.434

Gnomad OTH

AF:

0.527

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

GnomAD4 genome

AF:

0.543

AC:

74473

AN:

137042

Hom.:

20863

Cov.:

AF XY:

0.545

AC XY:

36325

AN XY:

66690

show subpopulations

African (AFR)

AF:

0.794

AC:

32006

AN:

40328

American (AMR)

AF:

0.429

AC:

5475

AN:

12768

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1492

AN:

3130

East Asian (EAS)

AF:

0.378

AC:

1560

AN:

4132

South Asian (SAS)

AF:

0.495

AC:

2295

AN:

4638

European-Finnish (FIN)

AF:

0.458

AC:

4131

AN:

9016

Middle Eastern (MID)

AF:

0.626

AC:

174

AN:

278

European-Non Finnish (NFE)

AF:

0.434

AC:

26045

AN:

59966

Other (OTH)

AF:

0.527

AC:

1011

AN:

1918

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

1590

3180

4771

6361

7951

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

638

1276

1914

2552

3190

<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:

0.425

Hom.:

6470

Bravo

AF:

0.499

Asia WGS

AF:

0.411

AC:

1422

AN:

3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.58

(source)

DANN

Benign

0.83

PhyloP100

-1.2

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