rs1530300

Variant names:

• chr8-128907212-T-C
• rs1530300
• ENST00000630386.2:n.506-2079A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630386.2(CCDC26):​n.506-2079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 151,884 control chromosomes in the GnomAD database, including 4,955 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 0.24 (4955 hom., cov: 31)
• Consequence: CCDC26 ENST00000630386.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205
• Publications: 12 publications found

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000630386.2	n.506-2079A>G		intron_variant	Intron 6 of 6	5
CCDC26	ENST00000643616.1	n.136+57318A>G		intron_variant	Intron 2 of 3
CCDC26	ENST00000644557.1	n.411-2044A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35968 AN: 151766 Hom.: 4958 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0382

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.237 AC: 35970 AN: 151884 Hom.: 4955 Cov.: 31 AF XY: 0.232 AC XY: 17239 AN XY: 74238

African (AFR) AF: 0.137 AC: 5696 AN: 41490

American (AMR) AF: 0.193 AC: 2952 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3462

East Asian (EAS) AF: 0.0379 AC: 196 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1111 AN: 4818

European-Finnish (FIN) AF: 0.242 AC: 2551 AN: 10558

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21692 AN: 67806

Other (OTH) AF: 0.242 AC: 510 AN: 2108

Alfa AF: 0.294 Hom.: 6875

Bravo AF: 0.226

Asia WGS AF: 0.154 AC: 540 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs1530300; hg19: chr8-129919458;