rs4733724

Variant names:

• chr8-129711482-A-G
• rs4733724
• ENST00000646849.1:n.48-4300T>C

Variant summary

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

The ENST00000646849.1(CCDC26):​n.48-4300T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,086 control chromosomes in the GnomAD database, including 17,239 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 (17239 hom., cov: 32)
• Consequence: CCDC26 ENST00000646849.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 21 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000646849.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000646849.1		n.48-4300T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60745 AN: 151968 Hom.: 17194 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.434

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: 0.400 AC: 60854 AN: 152086 Hom.: 17239 Cov.: 32 AF XY: 0.402 AC XY: 29855 AN XY: 74354

African (AFR) AF: 0.772 AC: 32050 AN: 41490

American (AMR) AF: 0.408 AC: 6242 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 542 AN: 3468

East Asian (EAS) AF: 0.716 AC: 3695 AN: 5160

South Asian (SAS) AF: 0.433 AC: 2084 AN: 4808

European-Finnish (FIN) AF: 0.168 AC: 1773 AN: 10578

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

European-Non Finnish (NFE) AF: 0.198 AC: 13488 AN: 67982

Other (OTH) AF: 0.377 AC: 796 AN: 2114

Alfa AF: 0.262 Hom.: 20093

Bravo AF: 0.434

Asia WGS AF: 0.613 AC: 2130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.078
DANN	Benign	0.66
PhyloP100		-1.9

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: rs4733724;

hg19: chr8-130723728;