rs10505543

Variant names:

• chr8-129536787-G-A
• rs10505543
• ENST00000446592.7:n.313-56097C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-129536787-G-A
• chr8-129536787-G-C
• chr8-129536787-G-T

Variant summary

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

The ENST00000446592.7(CCDC26):​n.313-56097C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,266 control chromosomes in the GnomAD database, including 471 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 0.043 (471 hom., cov: 33)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.313-56097C>T		intron_variant	Intron 1 of 3
CCDC26	NR_130918.1	n.137+38095C>T		intron_variant	Intron 1 of 2
CCDC26	NR_130919.1	n.137+38095C>T		intron_variant	Intron 1 of 3
CCDC26	NR_130920.1	n.137+38095C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.313-56097C>T		intron_variant	Intron 1 of 3	1
CCDC26	ENST00000523151.6	n.135+38095C>T		intron_variant	Intron 1 of 2	1
CCDC26	ENST00000520048.1	n.110+38095C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6523 AN: 152148 Hom.: 468 Cov.: 33

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000294

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0429 AC: 6539 AN: 152266 Hom.: 471 Cov.: 33 AF XY: 0.0416 AC XY: 3094 AN XY: 74462

African (AFR) AF: 0.150 AC: 6215 AN: 41534

American (AMR) AF: 0.0153 AC: 234 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000622 AC: 3 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000294 AC: 20 AN: 68022

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.0271 Hom.: 77

Bravo AF: 0.0489

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10505543; hg19: chr8-130549033;