ENST00000593837.1:n.23+21535A>G

Variant names:

• chr3-107359050-T-C
• rs793534
• ENST00000593837.1:n.23+21535A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000593837.1(CCDC54-AS1):​n.23+21535A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.945 in 152,276 control chromosomes in the GnomAD database, including 68,251 homozygotes. 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 0.94 (68251 hom., cov: 32)
• Consequence: CCDC54-AS1 ENST00000593837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 1 publications found

Genes affected

CCDC54-AS1 (HGNC:56107): (CCDC54 antisense RNA 1)

DUBR (HGNC:48569): (DPPA2 upstream binding RNA) Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II; positive regulation of myoblast differentiation; and regulation of DNA methylation. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593837.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC54-AS1	ENST00000593837.1	TSL:5	n.23+21535A>G		intron	N/A
	CCDC54-AS1	ENST00000595232.2	TSL:5	n.488+21535A>G		intron	N/A
	CCDC54-AS1	ENST00000599431.3	TSL:5	n.405+21535A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.945 AC: 143763 AN: 152158 Hom.: 68195 Cov.: 32

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.944

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.945 AC: 143878 AN: 152276 Hom.: 68251 Cov.: 32 AF XY: 0.946 AC XY: 70473 AN XY: 74464

African (AFR) AF: 0.849 AC: 35239 AN: 41516

American (AMR) AF: 0.974 AC: 14902 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3333 AN: 3472

East Asian (EAS) AF: 0.944 AC: 4882 AN: 5172

South Asian (SAS) AF: 0.961 AC: 4633 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10595 AN: 10626

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67112 AN: 68042

Other (OTH) AF: 0.945 AC: 1999 AN: 2116

Alfa AF: 0.967 Hom.: 15586

Bravo AF: 0.938

Asia WGS AF: 0.948 AC: 3299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.64
DANN	Benign	0.75
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs793534; hg19: chr3-107077897;