rs759944

Variant names:

• chr8-128775180-A-G
• rs759944
• ENST00000643616.1:n.232+32894T>C

Your query was ambiguous. Multiple possible variants found:

• chr8-128775180-A-G
• chr8-128775180-A-T

Variant summary

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

The ENST00000643616.1(CCDC26):​n.232+32894T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,954 control chromosomes in the GnomAD database, including 18,620 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 0.49 (18620 hom., cov: 31)
• Consequence: CCDC26 ENST00000643616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.607 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	ENST00000643616.1	n.232+32894T>C		intron_variant	Intron 3 of 3
CCDC26	ENST00000675388.1	n.797+32894T>C		intron_variant	Intron 8 of 8
CCDC26	ENST00000676248.1	n.325+32894T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73815 AN: 151836 Hom.: 18606 Cov.: 31

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.486 AC: 73881 AN: 151954 Hom.: 18620 Cov.: 31 AF XY: 0.479 AC XY: 35548 AN XY: 74272

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.478

Alfa AF: 0.474 Hom.: 2361

Bravo AF: 0.496

Asia WGS AF: 0.412 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs759944; hg19: chr8-129787426;