20-30393423-G-C

Variant names:

• chr20-30393423-G-C
• rs73621498
• ENST00000278882.8:n.418-128G>C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NR_003579.2(FRG1BP):​n.568-128G>C 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 0.044 (0 hom., cov: 36)
  • Exomes 𝑓: 0.041 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FRG1BP NR_003579.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.953

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 20-30393423-G-C is Benign according to our data. Variant chr20-30393423-G-C is described in ClinVar as [Benign]. Clinvar id is 982081.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRG1BP	NR_003579.2	n.568-128G>C		intron_variant	Intron 4 of 7
FRG1BP	NR_145491.1	n.568-128G>C		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRG1BP	ENST00000278882.8	n.418-128G>C		intron_variant	Intron 5 of 8	6

Frequencies

GnomAD3 genomes AF: 0.00 AC: 3282 AN: 75622 Hom.: 0 Cov.: 36 FAILED QC

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0352

Gnomad AMR AF: 0.0555

Gnomad ASJ AF: 0.0338

Gnomad EAS AF: 0.0598

Gnomad SAS AF: 0.0645

Gnomad FIN AF: 0.0551

Gnomad MID AF: 0.0724

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0441

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0413 AC: 26473 AN: 641562 Hom.: 0 AF XY: 0.0441 AC XY: 13823 AN XY: 313206

Gnomad4 AFR exome AF: 0.0536

Gnomad4 AMR exome AF: 0.0904

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.0392

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.0309

Gnomad4 OTH exome AF: 0.0652

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0437 AC: 3304 AN: 75690 Hom.: 0 Cov.: 36 AF XY: 0.0479 AC XY: 1760 AN XY: 36708

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.0558

Gnomad4 ASJ AF: 0.0338

Gnomad4 EAS AF: 0.0596

Gnomad4 SAS AF: 0.0656

Gnomad4 FIN AF: 0.0551

Gnomad4 NFE AF: 0.0349

Gnomad4 OTH AF: 0.0465

Alfa AF: 0.471 Hom.: 0

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	-0.90
CADD	Benign	0.32
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73621498; hg19: chr20-29628099;