Genetic Variant FGGY-DT:n.307+3225T>C (chr1-59199870-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000623433.4(FGGY-DT):n.307+3225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.567 in 152,042 control chromosomes in the GnomAD database, including 25,188 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 0.57 ( 25188 hom., cov: 32)

Consequence

FGGY-DT
ENST00000623433.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.898

Publications

5 publications found

Variant links:

Genes affected

FGGY-DT (HGNC:55265): (FGGY divergent transcript)

FGGY-DT links:

JUN-DT (HGNC:49450): (JUN divergent transcript)

JUN-DT links:

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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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.674 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
FGGY-DT	ENST00000623433.4 link	n.307+3225T>C	intron_variant	Intron 2 of 3	5
FGGY-DT	ENST00000624265.3 link	n.111+8141T>C	intron_variant	Intron 1 of 2	5
FGGY-DT	ENST00000624582.3 link	n.374+3225T>C	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.567

AC:

86150

AN:

151924

Hom.:

25178

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.730

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.662

Gnomad EAS

AF:

0.529

Gnomad SAS

AF:

0.658

Gnomad FIN

AF:

0.641

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.604

Gnomad OTH

AF:

0.609

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

GnomAD4 genome

AF:

0.567

AC:

86181

AN:

152042

Hom.:

25188

Cov.:

AF XY:

0.572

AC XY:

42537

AN XY:

74304

show subpopulations

African (AFR)

AF:

0.423

AC:

17561

AN:

41482

American (AMR)

AF:

0.685

AC:

10468

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.662

AC:

2297

AN:

3470

East Asian (EAS)

AF:

0.531

AC:

2741

AN:

5166

South Asian (SAS)

AF:

0.658

AC:

3170

AN:

4820

European-Finnish (FIN)

AF:

0.641

AC:

6762

AN:

10546

Middle Eastern (MID)

AF:

0.690

AC:

203

AN:

294

European-Non Finnish (NFE)

AF:

0.604

AC:

41028

AN:

67958

Other (OTH)

AF:

0.608

AC:

1285

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1847

3694

5541

7388

9235

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

742

1484

2226

2968

3710

<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:

0.595

Hom.:

122308

Bravo

AF:

0.566

Asia WGS

AF:

0.598

AC:

2078

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.5

(source)

DANN

Benign

0.73

PhyloP100

0.90

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