3-107360387-A-G

Variant names:

• chr3-107360387-A-G
• rs709552
• ENST00000593837.1:n.23+20198T>C

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+20198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,134 control chromosomes in the GnomAD database, including 67,409 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 (67409 hom., cov: 30)
• Consequence: CCDC54-AS1 ENST00000593837.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22
• 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=-0.95).
• 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+20198T>C		intron_variant	Intron 1 of 2	5
CCDC54-AS1	ENST00000595232.2	n.488+20198T>C		intron_variant	Intron 3 of 3	5
CCDC54-AS1	ENST00000599431.3	n.405+20198T>C		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142686 AN: 152016 Hom.: 67353 Cov.: 30

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.944

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: 0.939 AC: 142801 AN: 152134 Hom.: 67409 Cov.: 30 AF XY: 0.941 AC XY: 69977 AN XY: 74380

African (AFR) AF: 0.827 AC: 34298 AN: 41450

American (AMR) AF: 0.970 AC: 14819 AN: 15276

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

East Asian (EAS) AF: 0.945 AC: 4871 AN: 5156

South Asian (SAS) AF: 0.961 AC: 4628 AN: 4816

European-Finnish (FIN) AF: 0.997 AC: 10587 AN: 10618

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

European-Non Finnish (NFE) AF: 0.986 AC: 67094 AN: 68026

Other (OTH) AF: 0.940 AC: 1990 AN: 2116

Alfa AF: 0.960 Hom.: 3693

Bravo AF: 0.931

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	-0.95
CADD	Benign	0.27
DANN	Benign	0.61
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs709552; hg19: chr3-107079234;