rs3857888

chr8-128812615-G-Cchr8-128812615-G-T

Variant summary

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

The ENST00000675388.1(CCDC26):n.701+4032C>G 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 0.395 in 151,956 control chromosomes in the GnomAD database, including 12,291 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 0.40 (12291 hom., cov: 32)
• Consequence: CCDC26 ENST00000675388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.715

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC26	ENST00000675388.1	n.701+4032C>G		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000643616.1	n.137-4446C>G		intron_variant, non_coding_transcript_variant
CCDC26	ENST00000676248.1	n.178+1846C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60024 AN: 151838 Hom.: 12282 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.395 AC: 60046 AN: 151956 Hom.: 12291 Cov.: 32 AF XY: 0.388 AC XY: 28852 AN XY: 74268

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.408

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.406

Alfa AF: 0.269 Hom.: 645

Bravo AF: 0.391

Asia WGS AF: 0.313 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	5.2
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3857888; hg19: chr8-129824861;