ENST00000593837.1:n.23+9011T>A

Variant names:

• chr3-107371574-A-T
• rs697965
• ENST00000593837.1:n.23+9011T>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+9011T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 152,182 control chromosomes in the GnomAD database, including 67,567 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 (67567 hom., cov: 30)
• Consequence: CCDC54-AS1 ENST00000593837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• 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 -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 = 0.981 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+9011T>A		intron_variant	Intron 1 of 2	5
CCDC54-AS1	ENST00000595232.2	n.488+9011T>A		intron_variant	Intron 3 of 3	5
CCDC54-AS1	ENST00000599431.3	n.405+9011T>A		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.940 AC: 142884 AN: 152064 Hom.: 67511 Cov.: 30

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.933

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.940 AC: 142999 AN: 152182 Hom.: 67567 Cov.: 30 AF XY: 0.942 AC XY: 70061 AN XY: 74396

African (AFR) AF: 0.830 AC: 34411 AN: 41454

American (AMR) AF: 0.970 AC: 14852 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3334 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4885 AN: 5172

South Asian (SAS) AF: 0.962 AC: 4634 AN: 4816

European-Finnish (FIN) AF: 0.997 AC: 10581 AN: 10614

Middle Eastern (MID) AF: 0.932 AC: 272 AN: 292

European-Non Finnish (NFE) AF: 0.987 AC: 67135 AN: 68036

Other (OTH) AF: 0.942 AC: 1987 AN: 2110

Alfa AF: 0.969 Hom.: 3929

Bravo AF: 0.932

Asia WGS AF: 0.947 AC: 3294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.1
DANN	Benign	0.73
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs697965; hg19: chr3-107090421;