8-129511191-A-G

Position:

• chr8-129511191-A-G

Variant summary

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

The NR_130917.1(CCDC26):​n.313-30501T>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 0.0565 in 152,176 control chromosomes in the GnomAD database, including 403 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 0.057 (403 hom., cov: 32)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

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 (EAS) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.313-30501T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.137+63691T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.137+63691T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.137+63691T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.135-30501T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0566 AC: 8601 AN: 152058 Hom.: 403 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0799

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0390

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0565 AC: 8598 AN: 152176 Hom.: 403 Cov.: 32 AF XY: 0.0592 AC XY: 4402 AN XY: 74388

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0800

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.0390

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0577 Hom.: 81

Bravo AF: 0.0574

Asia WGS AF: 0.221 AC: 764 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505540; hg19: chr8-130523437;