rs9642889

Positions:

• chr8-129224640-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000509893.3(CCDC26):​n.81-1271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,996 control chromosomes in the GnomAD database, including 10,957 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 0.37 (10957 hom., cov: 32)
• Consequence: CCDC26 ENST00000509893.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

Genes affected

CCDC26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00977	NR_033916.1	n.65-1271C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000509893.3	n.81-1271C>T		intron_variant		2
CCDC26	ENST00000644194.1	n.294-30058C>T		intron_variant
CCDC26	ENST00000644557.1	n.311-122251C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56444 AN: 151876 Hom.: 10922 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.372 AC: 56541 AN: 151996 Hom.: 10957 Cov.: 32 AF XY: 0.378 AC XY: 28050 AN XY: 74282

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.444

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.389

Alfa AF: 0.339 Hom.: 1118

Bravo AF: 0.379

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9642889; hg19: chr8-130236886;