8-129418444-A-T

Position:

• chr8-129418444-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

CCDC26 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.361-48067T>A		intron_variant
CCDC26	NR_130918.1	n.138-48067T>A		intron_variant
CCDC26	NR_130919.1	n.138-18760T>A		intron_variant
CCDC26	NR_130920.1	n.138-18760T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.361-48067T>A		intron_variant		1
CCDC26	ENST00000523151.6	n.136-48067T>A		intron_variant		1
ENSG00000253926	ENST00000519048.1	n.79+2417A>T		intron_variant		3

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

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.652

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.620

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1347053; hg19: chr8-130430690;