Genetic Variant FRG1BP:n.418-99C>A (chr20-30393452-C-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NR_003579.2(FRG1BP):n.568-99C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 28)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FRG1BP
NR_003579.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.384

Publications

0 publications found

Variant links:

Genes affected

FRG1BP (HGNC:15792): (FSHD region gene 1 family member B, pseudogene)

FRG1BP links:

FRG1BP (HGNC:):

FRG1BP links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_003579.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1BP	NR_003579.2		n.568-99C>A		intron	N/A
	FRG1BP	NR_145491.1		n.568-99C>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FRG1BP	ENST00000278882.8	TSL:6	n.418-99C>A	intron	N/A
FRG1BP	ENST00000829738.1		n.854-99C>A	intron	N/A
FRG1BP	ENST00000829739.1		n.878-99C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

83810

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1191132

Hom.:

AF XY:

0.00

AC XY:

AN XY:

584474

African (AFR)

AF:

0.00

AC:

AN:

25426

American (AMR)

AF:

0.00

AC:

AN:

22500

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19232

East Asian (EAS)

AF:

0.00

AC:

AN:

30288

South Asian (SAS)

AF:

0.00

AC:

AN:

58442

European-Finnish (FIN)

AF:

0.00

AC:

AN:

41958

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4922

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

939872

Other (OTH)

AF:

0.00

AC:

AN:

48492

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

83810

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

40700

African (AFR)

AF:

0.00

AC:

AN:

24382

American (AMR)

AF:

0.00

AC:

AN:

8276

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1930

East Asian (EAS)

AF:

0.00

AC:

AN:

2756

South Asian (SAS)

AF:

0.00

AC:

AN:

2704

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5582

Middle Eastern (MID)

AF:

0.00

AC:

AN:

172

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

36464

Other (OTH)

AF:

0.00

AC:

AN:

1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.25

(source)

DANN

Benign

0.45

PhyloP100

-0.38

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over