3-112628232-A-G

Variant names:

• chr3-112628232-A-G
• rs10511316
• NM_199511.3:c.2035+1881T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_199511.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC80	NM_199511.3	MANE Select	c.2035+1881T>C		intron	N/A	NP_955805.1
	CCDC80	NM_199512.3		c.2035+1881T>C		intron	N/A	NP_955806.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC80	ENST00000206423.8	TSL:1 MANE Select	c.2035+1881T>C		intron	N/A	ENSP00000206423.3
	CCDC80	ENST00000439685.6	TSL:1	c.2035+1881T>C		intron	N/A	ENSP00000411814.2
	CCDC80	ENST00000461431.1	TSL:3	c.226+1881T>C		intron	N/A	ENSP00000420123.1

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

African (AFR) AF: 0.125 AC: 5180 AN: 41486

American (AMR) AF: 0.227 AC: 3470 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1257 AN: 3466

East Asian (EAS) AF: 0.116 AC: 598 AN: 5174

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4818

European-Finnish (FIN) AF: 0.308 AC: 3247 AN: 10554

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20717 AN: 67948

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.295 Hom.: 12236

Bravo AF: 0.231

Asia WGS AF: 0.222 AC: 773 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	17
DANN	Benign	0.69
PhyloP100		3.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10511316; hg19: chr3-112347079;