Genetic Variant ENST00000447198.2:n.203-3545A>G (chr7-80266903-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 ENST00000447198.2(ENSG00000232667):n.203-3545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,036 control chromosomes in the GnomAD database, including 1,970 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 0.15 ( 1970 hom., cov: 32)

Consequence

ENSG00000232667
ENST00000447198.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.50

Publications

3 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=-0.88).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 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	ENST00000447198.2 link	n.203-3545A>G	intron_variant	Intron 2 of 4	5
ENSG00000232667	ENST00000617602.5 link	n.621-3545A>G	intron_variant	Intron 5 of 5	5
ENSG00000232667	ENST00000718128.1 link	n.458-3545A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.153

AC:

23315

AN:

151918

Hom.:

1973

Cov.:

show subpopulations

Gnomad AFR

AF:

0.119

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.00154

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.139

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.165

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

GnomAD4 genome

AF:

0.153

AC:

23310

AN:

152036

Hom.:

1970

Cov.:

AF XY:

0.149

AC XY:

11081

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.119

AC:

4935

AN:

41532

American (AMR)

AF:

0.138

AC:

2098

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

826

AN:

3468

East Asian (EAS)

AF:

0.00154

AC:

AN:

5180

South Asian (SAS)

AF:

0.121

AC:

584

AN:

4822

European-Finnish (FIN)

AF:

0.139

AC:

1469

AN:

10596

Middle Eastern (MID)

AF:

0.262

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12718

AN:

67884

Other (OTH)

AF:

0.163

AC:

344

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

991

1982

2972

3963

4954

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

264

528

792

1056

1320

<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:

0.162

Hom.:

1671

Bravo

AF:

0.151

Asia WGS

AF:

0.0620

AC:

217

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.6

(source)

DANN

Benign

0.75

PhyloP100

-1.5

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