rs891835

Positions:

• chr8-129479506-T-G

Variant summary

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

The NR_130917.1(CCDC26):​n.360+1137A>C 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 0.175 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 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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=-0.79).
• 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/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+1137A>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.137+95376A>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.138-79822A>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.138-79822A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000675388.1	n.182+1137A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.177

Alfa AF: 0.214 Hom.: 5770

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs891835; hg19: chr8-130491752;