rs999877

Variant names:

• chr8-129477967-G-T
• rs999877
• ENST00000446592.7:n.360+2676C>A

Variant summary

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

The ENST00000446592.7(CCDC26):​n.360+2676C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,064 control chromosomes in the GnomAD database, including 7,162 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 0.30 (7162 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.709
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.360+2676C>A		intron	N/A
	CCDC26	NR_130918.1		n.137+96915C>A		intron	N/A
	CCDC26	NR_130919.1		n.138-78283C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.360+2676C>A		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.135+96915C>A		intron	N/A
	CCDC26	ENST00000520048.1	TSL:3	n.111-78283C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45384 AN: 151946 Hom.: 7157 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.299 AC: 45403 AN: 152064 Hom.: 7162 Cov.: 32 AF XY: 0.299 AC XY: 22254 AN XY: 74308

African (AFR) AF: 0.285 AC: 11824 AN: 41478

American (AMR) AF: 0.280 AC: 4277 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3464

East Asian (EAS) AF: 0.131 AC: 679 AN: 5178

South Asian (SAS) AF: 0.174 AC: 837 AN: 4820

European-Finnish (FIN) AF: 0.410 AC: 4330 AN: 10552

Middle Eastern (MID) AF: 0.229 AC: 67 AN: 292

European-Non Finnish (NFE) AF: 0.320 AC: 21753 AN: 67980

Other (OTH) AF: 0.280 AC: 591 AN: 2112

Alfa AF: 0.329 Hom.: 1091

Bravo AF: 0.290

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.35
PhyloP100		-0.71

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: rs999877;

hg19: chr8-130490213;