20-30391112-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NR_003579.2(FRG1BP):​n.456-85C>T 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 0.50 ( 1 hom., cov: 93)
Exomes 𝑓: 0.51 ( 6443 hom. )
Failed GnomAD Quality Control

Consequence

FRG1BP
NR_003579.2 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.91
Variant links:
Genes affected
FRG1BP (HGNC:15792): (FSHD region gene 1 family member B, pseudogene)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
Variant 20-30391112-C-T is Benign according to our data. Variant chr20-30391112-C-T is described in ClinVar as [Benign]. Clinvar id is 982080.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FRG1BPNR_003579.2 linkn.456-85C>T intron_variant Intron 3 of 7
FRG1BPNR_145491.1 linkn.456-85C>T intron_variant Intron 3 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FRG1BPENST00000278882.8 linkn.306-85C>T intron_variant Intron 4 of 8 6

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
76155
AN:
152308
Hom.:
1
Cov.:
93
FAILED QC
Gnomad AFR
AF:
0.500
Gnomad AMI
AF:
0.500
Gnomad AMR
AF:
0.500
Gnomad ASJ
AF:
0.500
Gnomad EAS
AF:
0.500
Gnomad SAS
AF:
0.500
Gnomad FIN
AF:
0.500
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.500
Gnomad OTH
AF:
0.500
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.507
AC:
306949
AN:
605472
Hom.:
6443
AF XY:
0.507
AC XY:
163038
AN XY:
321634
show subpopulations
Gnomad4 AFR exome
AF:
0.502
Gnomad4 AMR exome
AF:
0.489
Gnomad4 ASJ exome
AF:
0.504
Gnomad4 EAS exome
AF:
0.507
Gnomad4 SAS exome
AF:
0.494
Gnomad4 FIN exome
AF:
0.508
Gnomad4 NFE exome
AF:
0.510
Gnomad4 OTH exome
AF:
0.511
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.500
AC:
76214
AN:
152426
Hom.:
1
Cov.:
93
AF XY:
0.500
AC XY:
37273
AN XY:
74544
show subpopulations
Gnomad4 AFR
AF:
0.500
Gnomad4 AMR
AF:
0.500
Gnomad4 ASJ
AF:
0.500
Gnomad4 EAS
AF:
0.500
Gnomad4 SAS
AF:
0.500
Gnomad4 FIN
AF:
0.500
Gnomad4 NFE
AF:
0.500
Gnomad4 OTH
AF:
0.500
Alfa
AF:
0.500
Hom.:
2

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
-0.91
CADD
Benign
0.11
DANN
Benign
0.28

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.

Other links and lift over

dbSNP: rs4635596; hg19: chr20-29625788; API