rs999877

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+2676C>A		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.137+96915C>A		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-78283C>A		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-78283C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.360+2676C>A		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.135+96915C>A		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-78283C>A		intron_variant	Intron 1 of 3	3

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

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.280

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.280

Alfa AF: 0.330 Hom.: 1059

Bravo AF: 0.290

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs999877; hg19: chr8-130490213;