chr20-30391112-C-T

Variant names:

• chr20-30391112-C-T
• rs4635596
• ENST00000278882.8:n.306-85C>T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_Strong BP6_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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.91
• Publications: 2 publications found

Genes affected

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

FRG1BP (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -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 VariationId is 982080.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.456-85C>T		intron	N/A
	FRG1BP	NR_145491.1		n.456-85C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1BP	ENST00000278882.8	TSL:6	n.306-85C>T		intron	N/A
	FRG1BP	ENST00000829738.1		n.742-85C>T		intron	N/A
	FRG1BP	ENST00000829739.1		n.766-85C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.500 AC: 76155 AN: 152308 Hom.: 1 Cov.: 93

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

African (AFR) AF: 0.502 AC: 7628 AN: 15188

American (AMR) AF: 0.489 AC: 13787 AN: 28186

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 8664 AN: 17180

East Asian (EAS) AF: 0.507 AC: 16224 AN: 32024

South Asian (SAS) AF: 0.494 AC: 28015 AN: 56714

European-Finnish (FIN) AF: 0.508 AC: 23132 AN: 45524

Middle Eastern (MID) AF: 0.505 AC: 1857 AN: 3674

European-Non Finnish (NFE) AF: 0.510 AC: 191743 AN: 375886

Other (OTH) AF: 0.511 AC: 15899 AN: 31096

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

African (AFR) AF: 0.500 AC: 20805 AN: 41608

American (AMR) AF: 0.500 AC: 7657 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1736 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2598 AN: 5196

South Asian (SAS) AF: 0.500 AC: 2417 AN: 4834

European-Finnish (FIN) AF: 0.500 AC: 5315 AN: 10630

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34025 AN: 68050

Other (OTH) AF: 0.500 AC: 1058 AN: 2116

Alfa AF: 0.500 Hom.: 2

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.11
DANN	Benign	0.28
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs4635596; hg19: chr20-29625788;