rs6989059

Variant names:

• chr8-129105962-G-A
• rs6989059
• ENST00000644194.1:n.637-3573C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-129105962-G-A
• chr8-129105962-G-C
• chr8-129105962-G-T

Variant summary

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

The ENST00000644194.1(CCDC26):​n.637-3573C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,116 control chromosomes in the GnomAD database, including 4,015 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 0.19 (4015 hom., cov: 32)
• Consequence: CCDC26 ENST00000644194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.434
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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	ENST00000644194.1	n.637-3573C>T		intron_variant	Intron 3 of 6
CCDC26	ENST00000644557.1	n.311-3573C>T		intron_variant	Intron 2 of 3
CCDC26	ENST00000671439.1	n.315-3573C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29325 AN: 151998 Hom.: 3990 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0663

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.193 AC: 29394 AN: 152116 Hom.: 4015 Cov.: 32 AF XY: 0.191 AC XY: 14216 AN XY: 74364

African (AFR) AF: 0.377 AC: 15627 AN: 41478

American (AMR) AF: 0.181 AC: 2768 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1518 AN: 5152

South Asian (SAS) AF: 0.202 AC: 975 AN: 4824

European-Finnish (FIN) AF: 0.0663 AC: 703 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6829 AN: 68014

Other (OTH) AF: 0.178 AC: 376 AN: 2108

Alfa AF: 0.128 Hom.: 1138

Bravo AF: 0.213

Asia WGS AF: 0.291 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6989059; hg19: chr8-130118208;