rs891835

Variant names:

• chr8-129479506-T-G
• rs891835
• ENST00000446592.7:n.360+1137A>C

Variant summary

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

The ENST00000446592.7(CCDC26):​n.360+1137A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,156 control chromosomes in the GnomAD database, including 3,024 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 0.18 (3024 hom., cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 35 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+1137A>C		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.137+95376A>C		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.138-79822A>C		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.138-79822A>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.360+1137A>C		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.135+95376A>C		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.111-79822A>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26663 AN: 152038 Hom.: 3025 Cov.: 31

Gnomad AFR AF: 0.0465

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.175 AC: 26661 AN: 152156 Hom.: 3024 Cov.: 31 AF XY: 0.180 AC XY: 13358 AN XY: 74394

African (AFR) AF: 0.0463 AC: 1925 AN: 41538

American (AMR) AF: 0.201 AC: 3077 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3468

East Asian (EAS) AF: 0.130 AC: 671 AN: 5162

South Asian (SAS) AF: 0.137 AC: 662 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3572 AN: 10560

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.228 AC: 15512 AN: 67986

Other (OTH) AF: 0.177 AC: 374 AN: 2114

Alfa AF: 0.208 Hom.: 12462

Bravo AF: 0.161

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.84
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs891835; hg19: chr8-130491752;