rs10511316

chr3-112628232-A-G

Variant summary

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

The NM_199511.3(CCDC80):c.2035+1881T>C variant causes a intron change. The variant allele was found at a frequency of 0.242 in 152,036 control chromosomes in the GnomAD database, including 5,016 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 0.24 (5016 hom., cov: 32)
• Consequence: CCDC80 NM_199511.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.71

Genes affected

CCDC80 (HGNC:30649): (coiled-coil domain containing 80) Predicted to enable glycosaminoglycan binding activity. Predicted to act upstream of or within extracellular matrix organization; positive regulation of cell-substrate adhesion; and response to bacterium. Predicted to be located in extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC80	NM_199511.3	c.2035+1881T>C		intron_variant		ENST00000206423.8
CCDC80	NM_199512.3	c.2035+1881T>C		intron_variant
CCDC80	XM_047447495.1	c.2068+1881T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC80	ENST00000206423.8	c.2035+1881T>C		intron_variant		1	NM_199511.3	P1
CCDC80	ENST00000439685.6	c.2035+1881T>C		intron_variant		1		P1
CCDC80	ENST00000461431.1	c.227+1881T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36801 AN: 151918 Hom.: 5018 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.242 AC: 36806 AN: 152036 Hom.: 5016 Cov.: 32 AF XY: 0.242 AC XY: 17979 AN XY: 74314

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.299

Alfa AF: 0.301 Hom.: 10049

Bravo AF: 0.231

Asia WGS AF: 0.222 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	17
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511316; hg19: chr3-112347079;