5-55248002-T-C

Variant names:

• chr5-55248002-T-C
• rs232315
• ENST00000506435.2:n.128+13962T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506435.2(CCNO-DT):​n.128+13962T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,098 control chromosomes in the GnomAD database, including 28,137 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 0.60 (28137 hom., cov: 33)
• Consequence: CCNO-DT ENST00000506435.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 publications found

Genes affected

CCNO-DT (HGNC:55543): (CCNO divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCNO-DT	NR_185977.1	n.147+13962T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCNO-DT	ENST00000506435.2	n.128+13962T>C		intron_variant	Intron 1 of 4	3
CCNO-DT	ENST00000749850.1	n.147+13962T>C		intron_variant	Intron 1 of 4
CCNO-DT	ENST00000749851.1	n.106+13962T>C		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90534 AN: 151980 Hom.: 28142 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.595 AC: 90559 AN: 152098 Hom.: 28137 Cov.: 33 AF XY: 0.590 AC XY: 43837 AN XY: 74346

African (AFR) AF: 0.419 AC: 17363 AN: 41486

American (AMR) AF: 0.589 AC: 9001 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2554 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2542 AN: 5148

South Asian (SAS) AF: 0.649 AC: 3134 AN: 4826

European-Finnish (FIN) AF: 0.565 AC: 5974 AN: 10570

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.704 AC: 47854 AN: 68006

Other (OTH) AF: 0.606 AC: 1277 AN: 2106

Alfa AF: 0.665 Hom.: 6996

Bravo AF: 0.588

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs232315; hg19: chr5-54543830;