chr8-128775180-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ENSG00000310114 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000643616.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000643616.1		n.232+32894T>C		intron	N/A
	CCDC26	ENST00000675388.1		n.797+32894T>C		intron	N/A
	CCDC26	ENST00000676248.1		n.325+32894T>C		intron	N/A

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

African (AFR) AF: 0.614 AC: 25434 AN: 41436

American (AMR) AF: 0.437 AC: 6665 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1448 AN: 3464

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5168

South Asian (SAS) AF: 0.434 AC: 2088 AN: 4814

European-Finnish (FIN) AF: 0.395 AC: 4172 AN: 10554

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31233 AN: 67940

Other (OTH) AF: 0.478 AC: 1006 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.53
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs759944; hg19: chr8-129787426;