rs4733718

Variant names:

• chr8-129634857-A-T
• rs4733718
• ENST00000446592.7:n.312+45071T>A

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+45071T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,964 control chromosomes in the GnomAD database, including 14,688 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 0.44 (14688 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. 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
	CCDC26	NR_130917.1		n.312+45071T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+45071T>A		intron	N/A
	CCDC26	ENST00000642958.2		n.474-6767T>A		intron	N/A
	CCDC26	ENST00000645432.1		n.363+45071T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66234 AN: 151846 Hom.: 14658 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 66313 AN: 151964 Hom.: 14688 Cov.: 32 AF XY: 0.435 AC XY: 32294 AN XY: 74310

African (AFR) AF: 0.510 AC: 21135 AN: 41420

American (AMR) AF: 0.448 AC: 6840 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2051 AN: 5152

South Asian (SAS) AF: 0.460 AC: 2219 AN: 4822

European-Finnish (FIN) AF: 0.382 AC: 4035 AN: 10564

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27555 AN: 67954

Other (OTH) AF: 0.430 AC: 905 AN: 2106

Alfa AF: 0.426 Hom.: 1779

Bravo AF: 0.443

Asia WGS AF: 0.447 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.64
PhyloP100		-0.17

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: rs4733718;

hg19: chr8-130647103;