rs1030626

Positions:

• chr8-129446893-G-C
• chr8-129446893-G-T

Variant summary

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

The NR_130917.1(CCDC26):​n.360+33750C>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 0.567 in 151,986 control chromosomes in the GnomAD database, including 24,678 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 0.57 (24678 hom., cov: 32)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.360+33750C>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.138-76516C>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.138-47209C>G		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.138-47209C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000675388.1	n.182+33750C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86196 AN: 151870 Hom.: 24673 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.567 AC: 86232 AN: 151986 Hom.: 24678 Cov.: 32 AF XY: 0.565 AC XY: 41974 AN XY: 74268

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.589

Alfa AF: 0.423 Hom.: 1087

Bravo AF: 0.582

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1030626; hg19: chr8-130459139;