8-129374488-G-C

Variant names:

• chr8-129374488-G-C
• rs16904056
• ENST00000446592.7:n.361-4111C>G

Variant summary

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

The ENST00000446592.7(CCDC26):​n.361-4111C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,022 control chromosomes in the GnomAD database, including 9,875 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 0.35 (9875 hom., cov: 32)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.361-4111C>G		intron_variant	Intron 2 of 3
CCDC26	NR_130918.1	n.138-4111C>G		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.292-4111C>G		intron_variant	Intron 2 of 3
CCDC26	NR_130920.1	n.309-4111C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.361-4111C>G		intron_variant	Intron 2 of 3	1
CCDC26	ENST00000523151.6	n.136-4111C>G		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.282-4111C>G		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52858 AN: 151904 Hom.: 9860 Cov.: 32

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.348 AC: 52905 AN: 152022 Hom.: 9875 Cov.: 32 AF XY: 0.346 AC XY: 25702 AN XY: 74320

African (AFR) AF: 0.485 AC: 20102 AN: 41446

American (AMR) AF: 0.284 AC: 4342 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1219 AN: 3464

East Asian (EAS) AF: 0.429 AC: 2219 AN: 5170

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2725 AN: 10562

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19536 AN: 67958

Other (OTH) AF: 0.333 AC: 705 AN: 2116

Alfa AF: 0.119 Hom.: 191

Bravo AF: 0.356

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs16904056; hg19: chr8-130386734;