3-107359640-C-T

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 ENST00000658011.1(CCDC54-AS1):​n.522+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 ENST00000658011.1 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658011.1. 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+20945G>A		intron	N/A
	CCDC54-AS1	ENST00000595232.2	TSL:5	n.488+20945G>A		intron	N/A
	CCDC54-AS1	ENST00000599431.3	TSL:5	n.405+20945G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs697963;

hg19: chr3-107078487;