20-30393452-C-G

Variant names:

• chr20-30393452-C-G
• rs73621500
• ENST00000278882.8:n.418-99C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NR_003579.2(FRG1BP):​n.568-99C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 28)
  • Exomes 𝑓: 0.0000017 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FRG1BP NR_003579.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• 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 -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

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.568-99C>G		intron	N/A
	FRG1BP	NR_145491.1		n.568-99C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1BP	ENST00000278882.8	TSL:6	n.418-99C>G		intron	N/A
	FRG1BP	ENST00000829738.1		n.854-99C>G		intron	N/A
	FRG1BP	ENST00000829739.1		n.878-99C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 83812 Hom.: 0 Cov.: 28

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000168 AC: 2 AN: 1191128 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 584472

African (AFR) AF: 0.00 AC: 0 AN: 25428

American (AMR) AF: 0.0000444 AC: 1 AN: 22500

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19232

East Asian (EAS) AF: 0.00 AC: 0 AN: 30288

South Asian (SAS) AF: 0.00 AC: 0 AN: 58442

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41956

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4922

European-Non Finnish (NFE) AF: 0.00000106 AC: 1 AN: 939868

Other (OTH) AF: 0.00 AC: 0 AN: 48492

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 83812 Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0 AN XY: 40704

African (AFR) AF: 0.00 AC: 0 AN: 24380

American (AMR) AF: 0.00 AC: 0 AN: 8276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1932

East Asian (EAS) AF: 0.00 AC: 0 AN: 2756

South Asian (SAS) AF: 0.00 AC: 0 AN: 2704

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5584

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 172

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 36464

Other (OTH) AF: 0.00 AC: 0 AN: 1118

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.28
DANN	Benign	0.61
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs73621500; hg19: chr20-29628128;