20-30393436-C-T

Variant names:

• chr20-30393436-C-T
• rs73621499
• ENST00000278882.8:n.418-115C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_003579.2(FRG1BP):​n.568-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000965 in 1,036,186 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 36)
  • Exomes 𝑓: 9.7e-7 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: FRG1BP NR_003579.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 0 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

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.568-115C>T		intron	N/A
	FRG1BP	NR_145491.1		n.568-115C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FRG1BP	ENST00000278882.8	TSL:6	n.418-115C>T		intron	N/A
	FRG1BP	ENST00000829738.1		n.854-115C>T		intron	N/A
	FRG1BP	ENST00000829739.1		n.878-115C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 123532 Hom.: 0 Cov.: 36

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 AF: 9.65e-7 AC: 1 AN: 1036186 Hom.: 0 AF XY: 0.00000196 AC XY: 1 AN XY: 510532

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 22050

American (AMR) AF: 0.00 AC: 0 AN: 17134

Ashkenazi Jewish (ASJ) AF: 0.0000617 AC: 1 AN: 16198

East Asian (EAS) AF: 0.00 AC: 0 AN: 27418

South Asian (SAS) AF: 0.00 AC: 0 AN: 51656

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37764

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4448

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 816912

Other (OTH) AF: 0.00 AC: 0 AN: 42606

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 123532 Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0 AN XY: 59526

African (AFR) AF: 0.00 AC: 0 AN: 33310

American (AMR) AF: 0.00 AC: 0 AN: 11798

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2922

East Asian (EAS) AF: 0.00 AC: 0 AN: 4272

South Asian (SAS) AF: 0.00 AC: 0 AN: 3798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7888

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 250

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 56874

Other (OTH) AF: 0.00 AC: 0 AN: 1678

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	-0.82
CADD	Benign	0.95
DANN	Benign	0.28
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs73621499; hg19: chr20-29628112;