Genetic Variant FRG1BP:n.726-104C>A (chr20-30399118-C-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NR_003579.2(FRG1BP):n.876-104C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 141,188 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.49 ( 0 hom., cov: 50)

Exomes 𝑓: 0.48 ( 7 hom. )

Failed GnomAD Quality Control

Consequence

FRG1BP
NR_003579.2 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.177

Variant links:

Genes affected

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

FRG1BP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

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

BP6

Variant 20-30399118-C-A is Benign according to our data. Variant chr20-30399118-C-A is described in ClinVar as [Benign]. Clinvar id is 982103.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRG1BP	NR_003579.2 link	n.876-104C>A		intron_variant	Intron 7 of 7
FRG1BP	NR_145491.1 link	n.875+1073C>A		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRG1BP	ENST00000278882.8 link	n.726-104C>A		intron_variant	Intron 8 of 8	6

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

70797

AN:

143864

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.477

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.490

GnomAD4 exome

AF:

0.478

AC:

67555

AN:

141188

Hom.:

AF XY:

0.476

AC XY:

38158

AN XY:

80226

show subpopulations

Gnomad4 AFR exome

AF:

0.481

Gnomad4 AMR exome

AF:

0.472

Gnomad4 ASJ exome

AF:

0.465

Gnomad4 EAS exome

AF:

0.479

Gnomad4 SAS exome

AF:

0.479

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.475

Gnomad4 OTH exome

AF:

0.478

GnomAD4 genome

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

AF:

0.492

AC:

70831

AN:

143954

Hom.:

Cov.:

AF XY:

0.491

AC XY:

34403

AN XY:

70126

show subpopulations

Gnomad4 AFR

AF:

0.497

Gnomad4 AMR

AF:

0.493

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.493

Gnomad4 SAS

AF:

0.497

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.490

Alfa

AF:

0.500

Hom.:

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Pathology and Clinical Laboratory Medicine, King Fahad Medical City

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

7.7

DANN

Benign

0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over