8-129673211-T-G

Variant names:

• chr8-129673211-T-G
• rs4295627
• ENST00000446592.7:n.312+6717A>C

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+6717A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,204 control chromosomes in the GnomAD database, including 2,405 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 0.17 (2405 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08
• Publications: 73 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.226 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+6717A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.312+6717A>C		intron	N/A
	CCDC26	ENST00000642958.2		n.374-4913A>C		intron	N/A
	CCDC26	ENST00000645432.1		n.363+6717A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26448 AN: 152086 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.174 AC: 26492 AN: 152204 Hom.: 2405 Cov.: 32 AF XY: 0.178 AC XY: 13270 AN XY: 74402

African (AFR) AF: 0.133 AC: 5512 AN: 41530

American (AMR) AF: 0.232 AC: 3545 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1217 AN: 5170

South Asian (SAS) AF: 0.179 AC: 863 AN: 4826

European-Finnish (FIN) AF: 0.221 AC: 2341 AN: 10586

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11917 AN: 68018

Other (OTH) AF: 0.172 AC: 364 AN: 2112

Alfa AF: 0.173 Hom.: 9030

Bravo AF: 0.178

Asia WGS AF: 0.185 AC: 646 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.059
DANN	Benign	0.50
PhyloP100		-2.1

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: rs4295627;

hg19: chr8-130685457;