8-129713419-C-T

Variant names:

• chr8-129713419-C-T
• rs6470764
• ENST00000646849.1:n.48-6237G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000646849.1(CCDC26):​n.48-6237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,990 control chromosomes in the GnomAD database, including 17,025 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 0.40 (17025 hom., cov: 32)
• Consequence: CCDC26 ENST00000646849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18
• Publications: 42 publications found

Genes affected

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

GSDMC (HGNC:7151): (gasdermin C) Predicted to enable phosphatidylinositol-4,5-bisphosphate binding activity; phosphatidylinositol-4-phosphate binding activity; and phosphatidylserine binding activity. Predicted to be involved in defense response to bacterium and pyroptosis. Predicted to act upstream of or within intestinal epithelial cell development. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSDMC	XR_928339.3	n.2054-6237G>A		intron_variant	Intron 14 of 15
GSDMC	XR_928340.3	n.2054-6237G>A		intron_variant	Intron 14 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000646849.1	n.48-6237G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60398 AN: 151872 Hom.: 16979 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.398 AC: 60510 AN: 151990 Hom.: 17025 Cov.: 32 AF XY: 0.400 AC XY: 29681 AN XY: 74270

African (AFR) AF: 0.766 AC: 31762 AN: 41454

American (AMR) AF: 0.407 AC: 6226 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3470

East Asian (EAS) AF: 0.717 AC: 3687 AN: 5144

South Asian (SAS) AF: 0.434 AC: 2089 AN: 4812

European-Finnish (FIN) AF: 0.168 AC: 1770 AN: 10554

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13451 AN: 67960

Other (OTH) AF: 0.378 AC: 799 AN: 2112

Alfa AF: 0.294 Hom.: 15554

Bravo AF: 0.432

Asia WGS AF: 0.614 AC: 2136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Benign	0.77
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs6470764; hg19: chr8-130725665;