ENST00000593837.1:n.23+20257C>T

Variant names:

• chr3-107360328-G-A
• rs709551
• ENST00000593837.1:n.23+20257C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000593837.1(CCDC54-AS1):​n.23+20257C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,260 control chromosomes in the GnomAD database, including 67,398 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 (67398 hom., cov: 31)
• Consequence: CCDC54-AS1 ENST00000593837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• 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+20257C>T		intron	N/A
	CCDC54-AS1	ENST00000595232.2	TSL:5	n.488+20257C>T		intron	N/A
	CCDC54-AS1	ENST00000599431.3	TSL:5	n.405+20257C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142727 AN: 152142 Hom.: 67342 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.938 AC: 142842 AN: 152260 Hom.: 67398 Cov.: 31 AF XY: 0.940 AC XY: 70014 AN XY: 74452

African (AFR) AF: 0.826 AC: 34290 AN: 41524

American (AMR) AF: 0.970 AC: 14833 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3332 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4885 AN: 5176

South Asian (SAS) AF: 0.961 AC: 4631 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10599 AN: 10630

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67104 AN: 68036

Other (OTH) AF: 0.940 AC: 1986 AN: 2112

Alfa AF: 0.955 Hom.: 8999

Bravo AF: 0.930

Asia WGS AF: 0.949 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	12
DANN	Benign	0.90
PhyloP100		-0.093

Splicing

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

Other links and lift over

dbSNP: rs709551; hg19: chr3-107079175;