rs16904092

Variant names:

• chr8-129489684-T-C
• rs16904092
• ENST00000446592.7:n.313-8994A>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.313-8994A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 152,008 control chromosomes in the GnomAD database, including 1,505 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 0.094 (1505 hom., cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	NR_130917.1		n.313-8994A>G		intron	N/A
	CCDC26	NR_130918.1		n.137+85198A>G		intron	N/A
	CCDC26	NR_130919.1		n.137+85198A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.313-8994A>G		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.135+85198A>G		intron	N/A
	CCDC26	ENST00000675072.1		n.274A>G		non_coding_transcript_exon	Exon 4 of 11

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 14197 AN: 151890 Hom.: 1490 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0710

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

GnomAD4 genome AF: 0.0937 AC: 14241 AN: 152008 Hom.: 1505 Cov.: 31 AF XY: 0.0930 AC XY: 6911 AN XY: 74338

African (AFR) AF: 0.258 AC: 10687 AN: 41416

American (AMR) AF: 0.0622 AC: 949 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0421 AC: 146 AN: 3466

East Asian (EAS) AF: 0.0973 AC: 503 AN: 5168

South Asian (SAS) AF: 0.0960 AC: 462 AN: 4812

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0168 AC: 1140 AN: 67980

Other (OTH) AF: 0.0712 AC: 150 AN: 2106

Alfa AF: 0.0373 Hom.: 920

Bravo AF: 0.104

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.53
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs16904092; hg19: chr8-130501930;