Genetic Variant FRG1BP:n.418-115C>A (chr20-30393436-C-A) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NR_003579.2(FRG1BP):n.568-115C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0029 ( 0 hom., cov: 36)

Exomes 𝑓: 0.0013 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

FRG1BP
NR_003579.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.211

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 -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 20-30393436-C-A is Benign according to our data. Variant chr20-30393436-C-A is described in ClinVar as Benign. ClinVar VariationId is 982082.Status of the report is criteria_provided_single_submitter, 1 stars.

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.568-115C>A		intron	N/A
	FRG1BP	NR_145491.1		n.568-115C>A		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FRG1BP	ENST00000278882.8	TSL:6	n.418-115C>A	intron	N/A
FRG1BP	ENST00000829738.1		n.854-115C>A	intron	N/A
FRG1BP	ENST00000829739.1		n.878-115C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.00287

AC:

305

AN:

106368

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00360

Gnomad AMI

AF:

0.00344

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.00158

Gnomad EAS

AF:

0.00158

Gnomad SAS

AF:

0.00393

Gnomad FIN

AF:

0.00752

Gnomad MID

AF:

0.00459

Gnomad NFE

AF:

0.00149

Gnomad OTH

AF:

0.00203

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00132

AC:

1351

AN:

1019788

Hom.:

AF XY:

0.00129

AC XY:

649

AN XY:

502010

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00227

AC:

AN:

21584

American (AMR)

AF:

0.00241

AC:

AN:

16626

Ashkenazi Jewish (ASJ)

AF:

0.00351

AC:

AN:

15684

East Asian (EAS)

AF:

0.00432

AC:

113

AN:

26152

South Asian (SAS)

AF:

0.000827

AC:

AN:

50808

European-Finnish (FIN)

AF:

0.00296

AC:

107

AN:

36142

Middle Eastern (MID)

AF:

0.00228

AC:

AN:

4382

European-Non Finnish (NFE)

AF:

0.00104

AC:

839

AN:

806766

Other (OTH)

AF:

0.00231

AC:

AN:

41644

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.238

Heterozygous variant carriers

235

471

706

942

1177

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00289

AC:

308

AN:

106414

Hom.:

Cov.:

AF XY:

0.00343

AC XY:

176

AN XY:

51280

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00366

AC:

107

AN:

29264

American (AMR)

AF:

0.00478

AC:

AN:

10050

Ashkenazi Jewish (ASJ)

AF:

0.00158

AC:

AN:

2524

East Asian (EAS)

AF:

0.00158

AC:

AN:

3794

South Asian (SAS)

AF:

0.00426

AC:

AN:

3286

European-Finnish (FIN)

AF:

0.00752

AC:

AN:

6778

Middle Eastern (MID)

AF:

0.00490

AC:

AN:

204

European-Non Finnish (NFE)

AF:

0.00149

AC:

AN:

48438

Other (OTH)

AF:

0.00201

AC:

AN:

1494

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.239

Heterozygous variant carriers

106

158

211

264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.126

Hom.:

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.74

(source)

DANN

Benign

0.30

PhyloP100

-0.21

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

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over