8-129447166-T-G

Variant names:

• chr8-129447166-T-G
• rs1368136
• ENST00000446592.7:n.360+33477A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000446592.7(CCDC26):​n.360+33477A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 4 publications found

Genes affected

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

ENSG00000253926 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+33477A>C		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.138-76789A>C		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-47482A>C		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-47482A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.360+33477A>C		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.136-76789A>C		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-47482A>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 8088

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.14
DANN	Benign	0.49
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1368136; hg19: chr8-130459412;