Genetic Variant FOXCUT:n.*14C>T (chr6-1607368-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652712.1(FOXCUT):n.*14C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,238 control chromosomes in the GnomAD database, including 976 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 0.10 ( 976 hom., cov: 33)

Consequence

FOXCUT
ENST00000652712.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.278

Publications

6 publications found

Variant links:

Genes affected

FOXCUT (HGNC:50650): (FOXC1 upstream transcript)

FOXCUT 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 (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FOXCUT	NR_125804.1 link	n.*10C>T		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXCUT	ENST00000652712.1 link	n.*14C>T		downstream_gene_variant
FOXCUT	ENST00000841111.1 link	n.*10C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

15404

AN:

152120

Hom.:

979

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0541

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.0808

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.242

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.109

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

GnomAD4 genome

AF:

0.101

AC:

15393

AN:

152238

Hom.:

976

Cov.:

AF XY:

0.105

AC XY:

7817

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.0541

AC:

2249

AN:

41538

American (AMR)

AF:

0.0807

AC:

1234

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.179

AC:

622

AN:

3472

East Asian (EAS)

AF:

0.243

AC:

1256

AN:

5178

South Asian (SAS)

AF:

0.222

AC:

1072

AN:

4826

European-Finnish (FIN)

AF:

0.129

AC:

1366

AN:

10594

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7270

AN:

68018

Other (OTH)

AF:

0.108

AC:

228

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

702

1403

2105

2806

3508

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.104

Hom.:

1608

Bravo

AF:

0.0943

Asia WGS

AF:

0.211

AC:

733

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

1.6

(source)

DANN

Benign

0.29

PhyloP100

-0.28

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