8-129357989-A-G

Variant names:

• chr8-129357989-A-G
• rs7846284
• ENST00000446592.7:n.432-5009T>C

Variant summary

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

The ENST00000446592.7(CCDC26):​n.432-5009T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,958 control chromosomes in the GnomAD database, including 29,442 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 0.62 (29442 hom., cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 6 publications found

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.432-5009T>C		intron	N/A
	CCDC26	NR_130918.1		n.209-5009T>C		intron	N/A
	CCDC26	NR_130919.1		n.363-5009T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.432-5009T>C		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.207-5009T>C		intron	N/A
	CCDC26	ENST00000520048.1	TSL:3	n.353-5009T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93452 AN: 151840 Hom.: 29413 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.615 AC: 93522 AN: 151958 Hom.: 29442 Cov.: 31 AF XY: 0.616 AC XY: 45769 AN XY: 74256

African (AFR) AF: 0.733 AC: 30381 AN: 41428

American (AMR) AF: 0.480 AC: 7324 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2042 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2430 AN: 5158

South Asian (SAS) AF: 0.557 AC: 2673 AN: 4800

European-Finnish (FIN) AF: 0.680 AC: 7176 AN: 10558

Middle Eastern (MID) AF: 0.620 AC: 181 AN: 292

European-Non Finnish (NFE) AF: 0.582 AC: 39541 AN: 67962

Other (OTH) AF: 0.603 AC: 1274 AN: 2114

Alfa AF: 0.583 Hom.: 117664

Bravo AF: 0.603

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.32
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs7846284; hg19: chr8-130370235;