rs16904140

Variant names:

• chr8-129653397-G-A
• rs16904140
• ENST00000446592.7:n.312+26531C>T

Variant summary

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

The ENST00000446592.7(CCDC26):​n.312+26531C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,164 control chromosomes in the GnomAD database, including 3,003 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 0.19 (3003 hom., cov: 33)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 6 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.312+26531C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+26531C>T		intron_variant	Intron 1 of 3	1
CCDC26	ENST00000642958.2	n.473+14802C>T		intron_variant	Intron 3 of 3
CCDC26	ENST00000645432.1	n.363+26531C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29042 AN: 152046 Hom.: 2992 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.191 AC: 29071 AN: 152164 Hom.: 3003 Cov.: 33 AF XY: 0.195 AC XY: 14498 AN XY: 74390

African (AFR) AF: 0.107 AC: 4442 AN: 41520

American (AMR) AF: 0.256 AC: 3917 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1217 AN: 5172

South Asian (SAS) AF: 0.199 AC: 961 AN: 4830

European-Finnish (FIN) AF: 0.230 AC: 2439 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14444 AN: 67988

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.207 Hom.: 7459

Bravo AF: 0.194

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.74
PhyloP100		-0.23
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: rs16904140; hg19: chr8-130665643;