rs7846684

Positions:

• chr8-129358168-C-T

Variant summary

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

The NR_130917.1(CCDC26):​n.432-5188G>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 0.588 in 151,992 control chromosomes in the GnomAD database, including 26,569 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 0.59 (26569 hom., cov: 31)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680

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 = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.432-5188G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.209-5188G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.363-5188G>A		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.380-5188G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.336+41363G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89311 AN: 151874 Hom.: 26557 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.588 AC: 89358 AN: 151992 Hom.: 26569 Cov.: 31 AF XY: 0.590 AC XY: 43852 AN XY: 74282

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.580

Alfa AF: 0.575 Hom.: 34446

Bravo AF: 0.572

Asia WGS AF: 0.520 AC: 1808 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	0.92
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7846684; hg19: chr8-130370414;