rs9642889

Variant names:

• chr8-129224640-G-A
• rs9642889
• ENST00000509893.4:n.98-1271C>T

Variant summary

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

The ENST00000509893.4(CCDC26):​n.98-1271C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,996 control chromosomes in the GnomAD database, including 10,957 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 0.37 (10957 hom., cov: 32)
• Consequence: CCDC26 ENST00000509893.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• Publications: 1 publications found

Genes affected

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

ENSG00000287785 (HGNC:):

LINC00977 (HGNC:48902): (long intergenic non-protein coding RNA 977)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000509893.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00977	NR_033916.1		n.65-1271C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000509893.4	TSL:2	n.98-1271C>T		intron	N/A
	CCDC26	ENST00000644194.1		n.294-30058C>T		intron	N/A
	CCDC26	ENST00000644557.1		n.311-122251C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56444 AN: 151876 Hom.: 10922 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.372 AC: 56541 AN: 151996 Hom.: 10957 Cov.: 32 AF XY: 0.378 AC XY: 28050 AN XY: 74282

African (AFR) AF: 0.439 AC: 18187 AN: 41414

American (AMR) AF: 0.444 AC: 6778 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3464

East Asian (EAS) AF: 0.506 AC: 2621 AN: 5178

South Asian (SAS) AF: 0.407 AC: 1961 AN: 4814

European-Finnish (FIN) AF: 0.339 AC: 3580 AN: 10560

Middle Eastern (MID) AF: 0.383 AC: 111 AN: 290

European-Non Finnish (NFE) AF: 0.310 AC: 21066 AN: 67978

Other (OTH) AF: 0.389 AC: 822 AN: 2114

Alfa AF: 0.339 Hom.: 1118

Bravo AF: 0.379

Asia WGS AF: 0.452 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.41
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9642889;

hg19: chr8-130236886;