Genetic Variant ENST00000623433.4:n.307+2997C>T (chr1-59200098-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 ENST00000623433.4(FGGY-DT):n.307+2997C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 152,228 control chromosomes in the GnomAD database, including 620 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 0.074 ( 620 hom., cov: 32)

Consequence

FGGY-DT
ENST00000623433.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.225

Publications

2 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:

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 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+2997C>T	intron_variant	Intron 2 of 3	5
FGGY-DT	ENST00000624265.3 link	n.111+7913C>T	intron_variant	Intron 1 of 2	5
FGGY-DT	ENST00000624582.3 link	n.374+2997C>T	intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.0737

AC:

11213

AN:

152110

Hom.:

619

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0567

Gnomad ASJ

AF:

0.0459

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0261

Gnomad FIN

AF:

0.0167

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0499

Gnomad OTH

AF:

0.0880

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

GnomAD4 genome

AF:

0.0739

AC:

11247

AN:

152228

Hom.:

620

Cov.:

AF XY:

0.0704

AC XY:

5243

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.152

AC:

6296

AN:

41500

American (AMR)

AF:

0.0568

AC:

869

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0459

AC:

159

AN:

3466

East Asian (EAS)

AF:

0.000964

AC:

AN:

5188

South Asian (SAS)

AF:

0.0259

AC:

125

AN:

4826

European-Finnish (FIN)

AF:

0.0167

AC:

177

AN:

10610

Middle Eastern (MID)

AF:

0.0952

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0499

AC:

3393

AN:

68018

Other (OTH)

AF:

0.0875

AC:

185

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

521

1041

1562

2082

2603

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

240

360

480

600

<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:

0.0618

Hom.:

1238

Bravo

AF:

0.0813

Asia WGS

AF:

0.0210

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.90

(source)

DANN

Benign

0.20

PhyloP100

-0.23

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