8-129418444-A-T

Variant names:

• chr8-129418444-A-T
• rs1347053
• ENST00000446592.7:n.361-48067T>A

Variant summary

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

The ENST00000446592.7(CCDC26):​n.361-48067T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 151,442 control chromosomes in the GnomAD database, including 26,769 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 0.59 (26769 hom., cov: 29)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.344
• Publications: 1 publications found

Genes affected

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

ENSG00000253926 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446592.7. 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
	CCDC26	NR_130917.1		n.361-48067T>A		intron	N/A
	CCDC26	NR_130918.1		n.138-48067T>A		intron	N/A
	CCDC26	NR_130919.1		n.138-18760T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC26	ENST00000446592.7	TSL:1	n.361-48067T>A		intron	N/A
	CCDC26	ENST00000523151.6	TSL:1	n.136-48067T>A		intron	N/A
	ENSG00000253926	ENST00000519048.1	TSL:3	n.79+2417A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88582 AN: 151324 Hom.: 26744 Cov.: 29

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.585 AC: 88652 AN: 151442 Hom.: 26769 Cov.: 29 AF XY: 0.579 AC XY: 42837 AN XY: 73952

African (AFR) AF: 0.720 AC: 29736 AN: 41288

American (AMR) AF: 0.641 AC: 9748 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3464

East Asian (EAS) AF: 0.652 AC: 3351 AN: 5138

South Asian (SAS) AF: 0.552 AC: 2643 AN: 4788

European-Finnish (FIN) AF: 0.389 AC: 4074 AN: 10476

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34822 AN: 67784

Other (OTH) AF: 0.620 AC: 1304 AN: 2104

Alfa AF: 0.540 Hom.: 2832

Bravo AF: 0.614

Asia WGS AF: 0.609 AC: 2118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.0
DANN	Benign	0.89
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1347053; hg19: chr8-130430690;