ENST00000593837.1:n.23+20945G>A

Variant names:

• chr3-107359640-C-T
• rs697963
• ENST00000593837.1:n.23+20945G>A

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+20945G>A 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 152,256 control chromosomes in the GnomAD database, including 68,247 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 (68247 hom., cov: 32)
• Consequence: CCDC54-AS1 ENST00000593837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• 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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC54-AS1	ENST00000593837.1	n.23+20945G>A		intron_variant	Intron 1 of 2	5
CCDC54-AS1	ENST00000595232.2	n.488+20945G>A		intron_variant	Intron 3 of 3	5
CCDC54-AS1	ENST00000599431.3	n.405+20945G>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.945 AC: 143756 AN: 152138 Hom.: 68193 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: 0.944

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.945 AC: 143869 AN: 152256 Hom.: 68247 Cov.: 32 AF XY: 0.946 AC XY: 70451 AN XY: 74442

African (AFR) AF: 0.849 AC: 35257 AN: 41528

American (AMR) AF: 0.974 AC: 14890 AN: 15294

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

East Asian (EAS) AF: 0.944 AC: 4884 AN: 5172

South Asian (SAS) AF: 0.961 AC: 4630 AN: 4818

European-Finnish (FIN) AF: 0.997 AC: 10585 AN: 10616

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

European-Non Finnish (NFE) AF: 0.986 AC: 67110 AN: 68038

Other (OTH) AF: 0.946 AC: 1997 AN: 2112

Alfa AF: 0.972 Hom.: 295825

Bravo AF: 0.938

Asia WGS AF: 0.949 AC: 3298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs697963; hg19: chr3-107078487;