chr3-107360328-G-A

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.

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+20257C>T		intron_variant	Intron 1 of 2	5
CCDC54-AS1	ENST00000595232.2	n.488+20257C>T		intron_variant	Intron 3 of 3	5
CCDC54-AS1	ENST00000599431.3	n.405+20257C>T		intron_variant	Intron 3 of 4	5

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 v4.3

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;