rs4733718

chr8-129634857-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_130917.1(CCDC26):n.312+45071T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,964 control chromosomes in the GnomAD database, including 14,688 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 0.44 (14688 hom., cov: 32)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.312+45071T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000446592.7	n.312+45071T>A		intron_variant, non_coding_transcript_variant		1
CCDC26	ENST00000642958.2	n.474-6767T>A		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000645432.1	n.363+45071T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66234 AN: 151846 Hom.: 14658 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.436 AC: 66313 AN: 151964 Hom.: 14688 Cov.: 32 AF XY: 0.435 AC XY: 32294 AN XY: 74310

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.460

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.430

Alfa AF: 0.426 Hom.: 1779

Bravo AF: 0.443

Asia WGS AF: 0.447 AC: 1557 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.5
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4733718; hg19: chr8-130647103;