rs7846284

chr8-129357989-A-Gchr8-129357989-A-T

Variant summary

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

The NR_130917.1(CCDC26):n.432-5009T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,958 control chromosomes in the GnomAD database, including 29,442 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 0.62 (29442 hom., cov: 31)
• Consequence: CCDC26 NR_130917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC26	NR_130917.1	n.432-5009T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130918.1	n.209-5009T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130919.1	n.363-5009T>C		intron_variant, non_coding_transcript_variant
CCDC26	NR_130920.1	n.380-5009T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.336+41542T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93452 AN: 151840 Hom.: 29413 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.615 AC: 93522 AN: 151958 Hom.: 29442 Cov.: 31 AF XY: 0.616 AC XY: 45769 AN XY: 74256

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.603

Alfa AF: 0.580 Hom.: 53543

Bravo AF: 0.603

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.8
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7846284; hg19: chr8-130370235;