rs16904092

chr8-129489684-T-C

Variant summary

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

The NR_130917.1(CCDC26):n.313-8994A>G 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 0.0937 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 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.313-8994A>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.137+85198A>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.137+85198A>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.137+85198A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.135-8994A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.0973

Gnomad4 SAS AF: 0.0960

Gnomad4 FIN AF: 0.0164

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0355 Hom.: 373

Bravo AF: 0.104

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.46
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16904092; hg19: chr8-130501930;